From ff19b768e003a9a437da2d0a955b5cd4610ba3de Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 19 Oct 2021 12:56:11 +0200 Subject: [PATCH 01/43] move files to topic folders --- .../record_from_simulations.rst | 0 .../stimulate_the_network.rst | 0 doc/userdoc/guides/index.rst | 29 ------------------ .../parallel_computing.rst | 0 .../built-in_timers.rst | 0 .../random_numbers.rst | 0 .../running_simulations.rst | 0 .../figures/conn1.png | Bin .../figures/conn2.png | Bin .../figures/conn2_a.png | Bin .../figures/conn2_b.png | Bin .../figures/conn2_c.png | Bin .../figures/conn3.png | Bin .../figures/conn4.png | Bin .../figures/conn5.png | Bin .../figures/conn6.png | Bin .../figures/conn_3d.png | Bin .../figures/layer1.png | Bin .../figures/layer2.png | Bin .../figures/layer3.png | Bin .../figures/layer3a.png | Bin .../figures/layer4.png | Bin .../figures/layer4_3d.png | Bin .../figures/layer4_3d_b.png | Bin .../figures/layer4b.png | Bin .../figures/player.png | Bin 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b/doc/userdoc/device_docs/record_from_simulations.rst similarity index 100% rename from doc/userdoc/guides/record_from_simulations.rst rename to doc/userdoc/device_docs/record_from_simulations.rst diff --git a/doc/userdoc/guides/stimulate_the_network.rst b/doc/userdoc/device_docs/stimulate_the_network.rst similarity index 100% rename from doc/userdoc/guides/stimulate_the_network.rst rename to doc/userdoc/device_docs/stimulate_the_network.rst diff --git a/doc/userdoc/guides/index.rst b/doc/userdoc/guides/index.rst deleted file mode 100644 index 304b84117e..0000000000 --- a/doc/userdoc/guides/index.rst +++ /dev/null @@ -1,29 +0,0 @@ -Guides -====== - -Here you can find details on a variety of topics in NEST. - -.. toctree:: - :maxdepth: 1 - :caption: In-depth guides to NEST - - connection_management - running_simulations - stimulate_the_network - record_from_simulations - weight_normalization - random_numbers - built-in_timers - Reference guide 2.x to 3.0 <../release_notes/v3.0/refguide_nest2_nest3> - spatially_structured_networks - parallel_computing - simulations_with_gap_junctions - simulations_with_precise_spike_times - using_nest_with_music - -.. toctree:: - :maxdepth: 1 - :caption: Model Details - - exact-integration - Multicompartment models and synaptic delays <../models/pp_cond_exp_mc_urbanczik> diff --git a/doc/userdoc/guides/parallel_computing.rst b/doc/userdoc/hpc_docs/parallel_computing.rst similarity index 100% rename from doc/userdoc/guides/parallel_computing.rst rename to doc/userdoc/hpc_docs/parallel_computing.rst diff --git a/doc/userdoc/guides/built-in_timers.rst b/doc/userdoc/network_docs/built-in_timers.rst similarity index 100% rename from doc/userdoc/guides/built-in_timers.rst rename to doc/userdoc/network_docs/built-in_timers.rst diff --git a/doc/userdoc/guides/random_numbers.rst b/doc/userdoc/network_docs/random_numbers.rst similarity index 100% rename from doc/userdoc/guides/random_numbers.rst rename to 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a/doc/userdoc/release_notes/v3.0/features/handling_connections.rst b/doc/userdoc/synapse_docs/handling_connections.rst similarity index 100% rename from doc/userdoc/release_notes/v3.0/features/handling_connections.rst rename to doc/userdoc/synapse_docs/handling_connections.rst diff --git a/doc/userdoc/guides/simulations_with_gap_junctions.rst b/doc/userdoc/synapse_docs/simulations_with_gap_junctions.rst similarity index 100% rename from doc/userdoc/guides/simulations_with_gap_junctions.rst rename to doc/userdoc/synapse_docs/simulations_with_gap_junctions.rst diff --git a/doc/userdoc/guides/weight_normalization.rst b/doc/userdoc/synapse_docs/weight_normalization.rst similarity index 100% rename from doc/userdoc/guides/weight_normalization.rst rename to doc/userdoc/synapse_docs/weight_normalization.rst From bc900d67d53eb323197fb033ebc2f863b48241b5 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 20 Oct 2021 14:47:36 +0200 Subject: [PATCH 02/43] add index page --- doc/userdoc/device_docs/index.rst | 7 +++++++ doc/userdoc/hpc_docs/index.rst | 7 +++++++ doc/userdoc/network_docs/index.rst | 12 ++++++++++++ doc/userdoc/neuron_docs/index.rst | 7 +++++++ doc/userdoc/synapse_docs/index.rst | 7 +++++++ 5 files changed, 40 insertions(+) create mode 100644 doc/userdoc/device_docs/index.rst create mode 100644 doc/userdoc/hpc_docs/index.rst create mode 100644 doc/userdoc/network_docs/index.rst create mode 100644 doc/userdoc/neuron_docs/index.rst create mode 100644 doc/userdoc/synapse_docs/index.rst diff --git a/doc/userdoc/device_docs/index.rst b/doc/userdoc/device_docs/index.rst new file mode 100644 index 0000000000..1aacce1f11 --- /dev/null +++ b/doc/userdoc/device_docs/index.rst @@ -0,0 +1,7 @@ +All about devices in NEST +========================= + +.. toctree:: + :glob: + + * diff --git a/doc/userdoc/hpc_docs/index.rst b/doc/userdoc/hpc_docs/index.rst new file mode 100644 index 0000000000..7db060cdda --- /dev/null +++ b/doc/userdoc/hpc_docs/index.rst @@ -0,0 +1,7 @@ +All about high performance computing +==================================== + +.. toctree:: + :glob: + + * diff --git a/doc/userdoc/network_docs/index.rst b/doc/userdoc/network_docs/index.rst new file mode 100644 index 0000000000..5e25174a20 --- /dev/null +++ b/doc/userdoc/network_docs/index.rst @@ -0,0 +1,12 @@ +Guides to set up networks in NEST +================================= + + +.. toctree:: + :maxdepth: + + running_simulations + random_numbers + built-in_timers + spatially_structured_networks/spatially_structured_networks + using_nest_with_music diff --git a/doc/userdoc/neuron_docs/index.rst b/doc/userdoc/neuron_docs/index.rst new file mode 100644 index 0000000000..2831f87fcc --- /dev/null +++ b/doc/userdoc/neuron_docs/index.rst @@ -0,0 +1,7 @@ +All about neurons in NEST +========================= + +.. toctree:: + :glob: + + * diff --git a/doc/userdoc/synapse_docs/index.rst b/doc/userdoc/synapse_docs/index.rst new file mode 100644 index 0000000000..9b293fb21b --- /dev/null +++ b/doc/userdoc/synapse_docs/index.rst @@ -0,0 +1,7 @@ +All about synapses and connections in NEST +========================================== + +.. toctree:: + :glob: + + * From e869578d14bfb170f9620716f31dc90ef84ab4d9 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 20 Oct 2021 14:48:00 +0200 Subject: [PATCH 03/43] change global table of contents --- doc/userdoc/contents.rst | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index a6a3ca51aa..5f4774cf29 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -9,12 +9,13 @@ Table of Contents :maxdepth: 1 :caption: User Documentation - Download Install - Configure - getting_started + HPC Configure + Neurons + Synapses + Devices + Networks tutorials/index - guides/index examples/index models/index nest_server From 5f42a3eb0d929a863d0ce90db829fb8d44863671 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 10 Nov 2021 11:18:20 +0100 Subject: [PATCH 04/43] reorganize structure of toc --- doc/userdoc/contents.rst | 48 ++++++++++++++++++++++++++++------------ 1 file changed, 34 insertions(+), 14 deletions(-) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index 5f4774cf29..1a3a3073e1 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -7,28 +7,48 @@ Table of Contents .. toctree:: :maxdepth: 1 - :caption: User Documentation + :caption: Get started - Install - HPC Configure - Neurons - Synapses - Devices - Networks + Install NEST tutorials/index - examples/index - models/index - nest_server + PyNEST example scripts + +.. toctree:: + :maxdepth: 1 + :caption: Your system setup + + Communicate with other tools + HPC optimization + Benchmarking + + +.. toctree:: + :maxdepth: 1 + :caption: Understand how NEST works + + NEST models - how they are used and how you can create your own + Neurons + Synapses and connections + Devices - record and stimulate + Networks - understand spatially structured networks + NEST simulations - Understand and evaluate how NEST behaves during a simulation + +.. toctree:: + :maxdepth: 1 + :caption: Reference material + ref_material/pynest_apis + Model directory - complete list of all neuron, synapse, and device models + Glossary - list of commonly used terms in NEST + Release notes - find out what's new and what's changed troubleshooting - getting_help - release_notes/index .. toctree:: - :maxdepth: 2 - :caption: Getting Involved + :maxdepth: 1 + :caption: Get involved Community + getting_help Contribute documentation_workflow/index Publications From afc45fb1a099c93172e8c03c11b2c9951602f35b Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 10 Nov 2021 11:19:00 +0100 Subject: [PATCH 05/43] reorganize docs, add coupling and behavior directories --- doc/userdoc/coupling_nest_docs/index.rst | 10 ++++++++++ .../using_nest_with_music.rst | 0 .../built-in_timers.rst | 0 doc/userdoc/nest_behavior_docs/index.rst | 18 ++++++++++++++++++ .../random_numbers.rst | 0 .../running_simulations.rst | 0 doc/userdoc/network_docs/index.rst | 3 --- 7 files changed, 28 insertions(+), 3 deletions(-) create mode 100644 doc/userdoc/coupling_nest_docs/index.rst rename doc/userdoc/{network_docs => coupling_nest_docs}/using_nest_with_music.rst (100%) rename doc/userdoc/{network_docs => nest_behavior_docs}/built-in_timers.rst (100%) create mode 100644 doc/userdoc/nest_behavior_docs/index.rst rename doc/userdoc/{network_docs => nest_behavior_docs}/random_numbers.rst (100%) rename doc/userdoc/{network_docs => nest_behavior_docs}/running_simulations.rst (100%) diff --git a/doc/userdoc/coupling_nest_docs/index.rst b/doc/userdoc/coupling_nest_docs/index.rst new file mode 100644 index 0000000000..4967c3c83e --- /dev/null +++ b/doc/userdoc/coupling_nest_docs/index.rst @@ -0,0 +1,10 @@ +Coupling NEST with other tools +============================== + +Transmit data +Communicate with other tools + +.. toctree:: + + ../nest_server + using_nest_with_music diff --git a/doc/userdoc/network_docs/using_nest_with_music.rst b/doc/userdoc/coupling_nest_docs/using_nest_with_music.rst similarity index 100% rename from doc/userdoc/network_docs/using_nest_with_music.rst rename to doc/userdoc/coupling_nest_docs/using_nest_with_music.rst diff --git a/doc/userdoc/network_docs/built-in_timers.rst b/doc/userdoc/nest_behavior_docs/built-in_timers.rst similarity index 100% rename from doc/userdoc/network_docs/built-in_timers.rst rename to doc/userdoc/nest_behavior_docs/built-in_timers.rst diff --git a/doc/userdoc/nest_behavior_docs/index.rst b/doc/userdoc/nest_behavior_docs/index.rst new file mode 100644 index 0000000000..2a89c33be2 --- /dev/null +++ b/doc/userdoc/nest_behavior_docs/index.rst @@ -0,0 +1,18 @@ +How NEST works +============== + + +* how to run simulations + +* built in timers + +* randomness in NEST + +* parallel computing > HPC + +* benchmarking > HPC + +* pinning threads > HPC + + + diff --git a/doc/userdoc/network_docs/random_numbers.rst b/doc/userdoc/nest_behavior_docs/random_numbers.rst similarity index 100% rename from doc/userdoc/network_docs/random_numbers.rst rename to doc/userdoc/nest_behavior_docs/random_numbers.rst diff --git a/doc/userdoc/network_docs/running_simulations.rst b/doc/userdoc/nest_behavior_docs/running_simulations.rst similarity index 100% rename from doc/userdoc/network_docs/running_simulations.rst rename to doc/userdoc/nest_behavior_docs/running_simulations.rst diff --git a/doc/userdoc/network_docs/index.rst b/doc/userdoc/network_docs/index.rst index 5e25174a20..f6c154e4be 100644 --- a/doc/userdoc/network_docs/index.rst +++ b/doc/userdoc/network_docs/index.rst @@ -6,7 +6,4 @@ Guides to set up networks in NEST :maxdepth: running_simulations - random_numbers - built-in_timers spatially_structured_networks/spatially_structured_networks - using_nest_with_music From 47c62056075c5538cf9085776066ad4dd71ccd5c Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 10 Nov 2021 12:12:09 +0100 Subject: [PATCH 06/43] add empty files for links; update contents to include dev space; outline dev space --- doc/userdoc/contents.rst | 15 +++++---- doc/userdoc/developer_space.rst | 41 ++++++++++++++++++++++++ doc/userdoc/hpc_docs/benchmarking.rst | 2 ++ doc/userdoc/hpc_docs/pinning-threads.rst | 2 ++ doc/userdoc/models/models-main.rst | 2 ++ 5 files changed, 55 insertions(+), 7 deletions(-) create mode 100644 doc/userdoc/developer_space.rst create mode 100644 doc/userdoc/hpc_docs/benchmarking.rst create mode 100644 doc/userdoc/hpc_docs/pinning-threads.rst create mode 100644 doc/userdoc/models/models-main.rst diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index 1a3a3073e1..db692b0286 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -15,18 +15,18 @@ Table of Contents .. toctree:: :maxdepth: 1 - :caption: Your system setup + :caption: Specialized setup of NEST Communicate with other tools HPC optimization - Benchmarking + Benchmarking .. toctree:: :maxdepth: 1 :caption: Understand how NEST works - NEST models - how they are used and how you can create your own + NEST models - how they are used and how you can create your own Neurons Synapses and connections Devices - record and stimulate @@ -42,15 +42,16 @@ Table of Contents Glossary - list of commonly used terms in NEST Release notes - find out what's new and what's changed troubleshooting + Command line help .. toctree:: :maxdepth: 1 - :caption: Get involved + :caption: Community - Community - getting_help + Contact us Contribute - documentation_workflow/index + Developer space + News and updates Publications NEST Initiative diff --git a/doc/userdoc/developer_space.rst b/doc/userdoc/developer_space.rst new file mode 100644 index 0000000000..ded546f363 --- /dev/null +++ b/doc/userdoc/developer_space.rst @@ -0,0 +1,41 @@ +Developer space +=============== + +Here is all documentation pertaining to the development of NEST. +It is documentation for anyone needing to touch the code or documentation (also includes SLI, since it is more complex +and likely used by developers or very advanced users). + + +* install and configure for developers + +* Workflows + + * documentation workflows + * git workflows + * pull request process contributor + * pull request process reviewer + * release workflow + * Working with IDEs + +* templates + + * pynest example + * pynest api + * PR template + +* styleguide and rules + + * code guidelines + * comments and docstring guidlines + * user level docs guide + * guidelines writing tests, benchmarks etc + +* doxygen + + * Doxyfile + * output of doxygen + +* SLI documentation + + * help generator + * guides . . . diff --git a/doc/userdoc/hpc_docs/benchmarking.rst b/doc/userdoc/hpc_docs/benchmarking.rst new file mode 100644 index 0000000000..3fb875b81a --- /dev/null +++ b/doc/userdoc/hpc_docs/benchmarking.rst @@ -0,0 +1,2 @@ +Benchmarking guide +================== diff --git a/doc/userdoc/hpc_docs/pinning-threads.rst b/doc/userdoc/hpc_docs/pinning-threads.rst new file mode 100644 index 0000000000..c1808ee9ff --- /dev/null +++ b/doc/userdoc/hpc_docs/pinning-threads.rst @@ -0,0 +1,2 @@ +Pinning threads +=============== diff --git a/doc/userdoc/models/models-main.rst b/doc/userdoc/models/models-main.rst new file mode 100644 index 0000000000..bb405f5205 --- /dev/null +++ b/doc/userdoc/models/models-main.rst @@ -0,0 +1,2 @@ +Models in NEST +============== From 93995689a36accfde3a8c5e4080274aa173f6165 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Thu, 18 Nov 2021 14:14:03 +0100 Subject: [PATCH 07/43] rename toc to shorter titles --- doc/userdoc/contents.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index db692b0286..1aa8acb01e 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -17,7 +17,7 @@ Table of Contents :maxdepth: 1 :caption: Specialized setup of NEST - Communicate with other tools + Connect to other tools HPC optimization Benchmarking @@ -26,21 +26,21 @@ Table of Contents :maxdepth: 1 :caption: Understand how NEST works - NEST models - how they are used and how you can create your own + NEST models Neurons Synapses and connections - Devices - record and stimulate - Networks - understand spatially structured networks - NEST simulations - Understand and evaluate how NEST behaves during a simulation + Devices + Spatially-structured networks + Simulation behavior .. toctree:: :maxdepth: 1 :caption: Reference material ref_material/pynest_apis - Model directory - complete list of all neuron, synapse, and device models - Glossary - list of commonly used terms in NEST - Release notes - find out what's new and what's changed + Model directory + Glossary + Release notes troubleshooting Command line help From 7c0f006036dac3dff4a29058146c851de1de5667 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Fri, 19 Nov 2021 19:03:21 +0100 Subject: [PATCH 08/43] remove non existent doc placeholders and add todo instead --- doc/userdoc/hpc_docs/benchmarking.rst | 2 -- doc/userdoc/hpc_docs/index.rst | 4 ++++ doc/userdoc/hpc_docs/pinning-threads.rst | 2 -- 3 files changed, 4 insertions(+), 4 deletions(-) delete mode 100644 doc/userdoc/hpc_docs/benchmarking.rst delete mode 100644 doc/userdoc/hpc_docs/pinning-threads.rst diff --git a/doc/userdoc/hpc_docs/benchmarking.rst b/doc/userdoc/hpc_docs/benchmarking.rst deleted file mode 100644 index 3fb875b81a..0000000000 --- a/doc/userdoc/hpc_docs/benchmarking.rst +++ /dev/null @@ -1,2 +0,0 @@ -Benchmarking guide -================== diff --git a/doc/userdoc/hpc_docs/index.rst b/doc/userdoc/hpc_docs/index.rst index 7db060cdda..e4743ee03f 100644 --- a/doc/userdoc/hpc_docs/index.rst +++ b/doc/userdoc/hpc_docs/index.rst @@ -5,3 +5,7 @@ All about high performance computing :glob: * + +.. todo:: + + Add pinning threads and benchmarking documentation here. diff --git a/doc/userdoc/hpc_docs/pinning-threads.rst b/doc/userdoc/hpc_docs/pinning-threads.rst deleted file mode 100644 index c1808ee9ff..0000000000 --- a/doc/userdoc/hpc_docs/pinning-threads.rst +++ /dev/null @@ -1,2 +0,0 @@ -Pinning threads -=============== From 6ae6f7292445828ce6261df572d584048412040c Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Fri, 19 Nov 2021 19:04:28 +0100 Subject: [PATCH 09/43] move nest-server --- doc/userdoc/{ => coupling_nest_docs}/nest_server.rst | 2 ++ 1 file changed, 2 insertions(+) rename doc/userdoc/{ => coupling_nest_docs}/nest_server.rst (99%) diff --git a/doc/userdoc/nest_server.rst b/doc/userdoc/coupling_nest_docs/nest_server.rst similarity index 99% rename from doc/userdoc/nest_server.rst rename to doc/userdoc/coupling_nest_docs/nest_server.rst index 5997259962..f61b262927 100644 --- a/doc/userdoc/nest_server.rst +++ b/doc/userdoc/coupling_nest_docs/nest_server.rst @@ -1,3 +1,5 @@ +.. _nest_server: + NEST Server =========== From 4049e2779fb7305abe42b098c92a3f694b5fae39 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Mon, 17 Jan 2022 21:16:16 +0100 Subject: [PATCH 10/43] set max depth to 1 --- doc/userdoc/coupling_nest_docs/index.rst | 1 + doc/userdoc/device_docs/index.rst | 1 + doc/userdoc/hpc_docs/index.rst | 1 + doc/userdoc/network_docs/index.rst | 2 +- doc/userdoc/neuron_docs/index.rst | 1 + doc/userdoc/synapse_docs/index.rst | 1 + 6 files changed, 6 insertions(+), 1 deletion(-) diff --git a/doc/userdoc/coupling_nest_docs/index.rst b/doc/userdoc/coupling_nest_docs/index.rst index 4967c3c83e..17d66af74d 100644 --- a/doc/userdoc/coupling_nest_docs/index.rst +++ b/doc/userdoc/coupling_nest_docs/index.rst @@ -5,6 +5,7 @@ Transmit data Communicate with other tools .. toctree:: + :maxdepth: 1 ../nest_server using_nest_with_music diff --git a/doc/userdoc/device_docs/index.rst b/doc/userdoc/device_docs/index.rst index 1aacce1f11..2bc2bb1cfe 100644 --- a/doc/userdoc/device_docs/index.rst +++ b/doc/userdoc/device_docs/index.rst @@ -2,6 +2,7 @@ All about devices in NEST ========================= .. toctree:: + :maxdepth: 1 :glob: * diff --git a/doc/userdoc/hpc_docs/index.rst b/doc/userdoc/hpc_docs/index.rst index e4743ee03f..e53766c52c 100644 --- a/doc/userdoc/hpc_docs/index.rst +++ b/doc/userdoc/hpc_docs/index.rst @@ -2,6 +2,7 @@ All about high performance computing ==================================== .. toctree:: + :maxdepth: 1 :glob: * diff --git a/doc/userdoc/network_docs/index.rst b/doc/userdoc/network_docs/index.rst index f6c154e4be..c7ec7f4356 100644 --- a/doc/userdoc/network_docs/index.rst +++ b/doc/userdoc/network_docs/index.rst @@ -3,7 +3,7 @@ Guides to set up networks in NEST .. toctree:: - :maxdepth: + :maxdepth: 1 running_simulations spatially_structured_networks/spatially_structured_networks diff --git a/doc/userdoc/neuron_docs/index.rst b/doc/userdoc/neuron_docs/index.rst index 2831f87fcc..4718a6b6cc 100644 --- a/doc/userdoc/neuron_docs/index.rst +++ b/doc/userdoc/neuron_docs/index.rst @@ -2,6 +2,7 @@ All about neurons in NEST ========================= .. toctree:: + :maxdepth: 1 :glob: * diff --git a/doc/userdoc/synapse_docs/index.rst b/doc/userdoc/synapse_docs/index.rst index 9b293fb21b..494f1e6c2f 100644 --- a/doc/userdoc/synapse_docs/index.rst +++ b/doc/userdoc/synapse_docs/index.rst @@ -2,6 +2,7 @@ All about synapses and connections in NEST ========================================== .. toctree:: + :maxdepth: 1 :glob: * From 534368af06de53015c2f754a480fdcabe6f8f6fa Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Mon, 17 Jan 2022 21:16:47 +0100 Subject: [PATCH 11/43] update main toc --- doc/userdoc/contents.rst | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index 1aa8acb01e..2907c437a3 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -13,6 +13,13 @@ Table of Contents tutorials/index PyNEST example scripts +.. toctree:: + :maxdepth: 1 + :caption: Release notes + + Release notes + + .. toctree:: :maxdepth: 1 :caption: Specialized setup of NEST @@ -31,7 +38,9 @@ Table of Contents Synapses and connections Devices Spatially-structured networks - Simulation behavior + Simulation behavior + Random numbers + Built-in timers .. toctree:: :maxdepth: 1 @@ -40,17 +49,21 @@ Table of Contents ref_material/pynest_apis Model directory Glossary - Release notes + +.. toctree:: + :maxdepth: 1 + :caption: Get help + troubleshooting Command line help + Contact us .. toctree:: :maxdepth: 1 :caption: Community - Contact us - Contribute - Developer space + Contribute + Developer space News and updates Publications NEST Initiative From 3912bdb12629346e60a3d2e38d582cdc1810b992 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Mon, 17 Jan 2022 21:17:33 +0100 Subject: [PATCH 12/43] move devdocs into user, and move all contributing and sli into it --- .../index.rst => devdoc/contribute.rst} | 6 ++- 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rename doc/{ => userdoc}/devdoc/static/img/MPI_backend_protocol_of_communication.svg (100%) rename doc/{ => userdoc}/devdoc/static/img/MPI_backend_state_Nest.svg (100%) rename doc/{ => userdoc}/devdoc/static/ulmet/MPI_backend_example_state_machine_communication_with_Nest.uxf (100%) rename doc/{ => userdoc}/devdoc/static/ulmet/MPI_backend_protocol_of_communication.uxf (100%) rename doc/{ => userdoc}/devdoc/static/ulmet/MPI_backend_state_Nest.uxf (100%) rename doc/userdoc/{contribute => devdoc}/templates/example_template.rst (100%) rename doc/userdoc/{contribute => devdoc}/templates/pyapi_template.rst (100%) rename doc/userdoc/{contribute => devdoc}/templates/pynest_api_template.py (100%) rename doc/userdoc/{contribute => devdoc}/templates/pynest_example_template.py (100%) rename doc/userdoc/{contribute => devdoc/workflows}/ci.rst (100%) rename doc/userdoc/{contribute => devdoc/workflows}/development_workflow.rst (100%) rename doc/userdoc/{ => devdoc/workflows}/documentation_workflow/developer_documentation_workflow.rst (100%) rename doc/userdoc/{ => devdoc/workflows}/documentation_workflow/index.rst (100%) rename doc/userdoc/{ => devdoc/workflows}/documentation_workflow/user_documentation_workflow.rst (100%) rename doc/userdoc/{contribute => devdoc/workflows}/nest_with_ides.rst (100%) delete mode 100644 doc/userdoc/developer_space.rst diff --git a/doc/userdoc/contribute/index.rst b/doc/userdoc/devdoc/contribute.rst similarity index 98% rename from doc/userdoc/contribute/index.rst rename to doc/userdoc/devdoc/contribute.rst index d5b4261927..26d0de8e74 100644 --- a/doc/userdoc/contribute/index.rst +++ b/doc/userdoc/devdoc/contribute.rst @@ -1,7 +1,7 @@ .. _contribute: -Contributing to NEST -==================== +Contribute to NEST +================== NEST draws its strength from the many people that use and improve it. We are happy to consider your contributions (e.g., new models, bug or @@ -71,3 +71,5 @@ Have a question? ---------------- If you want to get in contact with us, see our :ref:`community` page for ways you can reach us. + + diff --git a/doc/userdoc/contribute/code_review_guidelines.rst b/doc/userdoc/devdoc/guidelines/code_review_guidelines.rst similarity index 100% rename from doc/userdoc/contribute/code_review_guidelines.rst rename to doc/userdoc/devdoc/guidelines/code_review_guidelines.rst diff --git a/doc/userdoc/contribute/coding_guidelines_cpp.rst b/doc/userdoc/devdoc/guidelines/coding_guidelines_cpp.rst similarity index 100% rename from doc/userdoc/contribute/coding_guidelines_cpp.rst rename to doc/userdoc/devdoc/guidelines/coding_guidelines_cpp.rst diff --git a/doc/userdoc/contribute/mailing_list_guidelines.rst b/doc/userdoc/devdoc/guidelines/mailing_list_guidelines.rst similarity index 100% rename from doc/userdoc/contribute/mailing_list_guidelines.rst rename to doc/userdoc/devdoc/guidelines/mailing_list_guidelines.rst diff --git a/doc/userdoc/contribute/naming_conventions.rst b/doc/userdoc/devdoc/guidelines/naming_conventions.rst similarity index 100% rename from doc/userdoc/contribute/naming_conventions.rst rename to doc/userdoc/devdoc/guidelines/naming_conventions.rst diff --git a/doc/userdoc/contribute/styleguide/sample_doc.rst b/doc/userdoc/devdoc/guidelines/styleguide/sample_doc.rst similarity index 95% rename from doc/userdoc/contribute/styleguide/sample_doc.rst rename to doc/userdoc/devdoc/guidelines/styleguide/sample_doc.rst index 491137af08..29a4021a8f 100644 --- a/doc/userdoc/contribute/styleguide/sample_doc.rst +++ b/doc/userdoc/devdoc/guidelines/styleguide/sample_doc.rst @@ -1,3 +1,5 @@ +:orphan: + .. _sample_doc: Main title of document diff --git a/doc/userdoc/contribute/styleguide/styleguide.rst b/doc/userdoc/devdoc/guidelines/styleguide/styleguide.rst similarity index 100% rename from doc/userdoc/contribute/styleguide/styleguide.rst rename to doc/userdoc/devdoc/guidelines/styleguide/styleguide.rst diff --git a/doc/userdoc/contribute/styleguide/vim_support_sli.rst b/doc/userdoc/devdoc/guidelines/styleguide/vim_support_sli.rst similarity index 100% rename from doc/userdoc/contribute/styleguide/vim_support_sli.rst rename to doc/userdoc/devdoc/guidelines/styleguide/vim_support_sli.rst diff --git a/doc/userdoc/devdoc/index.rst b/doc/userdoc/devdoc/index.rst new file mode 100644 index 0000000000..2daaf7b098 --- /dev/null +++ b/doc/userdoc/devdoc/index.rst @@ -0,0 +1,51 @@ +Developer space +=============== + +Here is all documentation pertaining to the development of NEST. +It is documentation for anyone needing to touch the code or documentation (also includes SLI, since it is more complex +and likely used by developers or very advanced users). + + +.. toctree:: + :maxdepth: 1 + :caption: Install from source + + ../installation/linux_install + +.. toctree:: + :maxdepth: 1 + :caption: Workflows + :glob: + + workflows/* + + +.. toctree:: + :maxdepth: 1 + :caption: Guidelines + :glob: + + guidelines/* + guidelines/styleguide/styleguide + guidelines/styleguide/vim_support_sli + + +.. toctree:: + :maxdepth: 1 + :caption: Templates + :glob: + + templates/* + +.. toctree:: + :maxdepth: 1 + :caption: SLI docs + :glob: + + sli_docs/* + +.. toctree:: + :maxdepth: 1 + :caption: Doxygen output + + doxygen/ diff --git a/doc/userdoc/sli_docs/an-introduction-to-sli.rst b/doc/userdoc/devdoc/sli_docs/an-introduction-to-sli.rst similarity index 100% rename from doc/userdoc/sli_docs/an-introduction-to-sli.rst rename to doc/userdoc/devdoc/sli_docs/an-introduction-to-sli.rst diff --git a/doc/userdoc/sli_docs/first-steps.rst b/doc/userdoc/devdoc/sli_docs/first-steps.rst similarity index 100% rename from doc/userdoc/sli_docs/first-steps.rst rename to doc/userdoc/devdoc/sli_docs/first-steps.rst diff --git a/doc/userdoc/devdoc/sli_docs/index.rst b/doc/userdoc/devdoc/sli_docs/index.rst new file mode 100644 index 0000000000..c162685532 --- /dev/null +++ b/doc/userdoc/devdoc/sli_docs/index.rst @@ -0,0 +1,14 @@ +SLI documentation +================= + + +.. toctree:: + :maxdepth: 1 + + an-introduction-to-sli + first-steps + neural-simulations + objects-and-data-types + programming-in-sli + using-files-and-keyboard-input + diff --git a/doc/userdoc/sli_docs/neural-simulations.rst b/doc/userdoc/devdoc/sli_docs/neural-simulations.rst similarity index 100% rename from doc/userdoc/sli_docs/neural-simulations.rst rename to doc/userdoc/devdoc/sli_docs/neural-simulations.rst diff --git a/doc/userdoc/sli_docs/objects-and-data-types.rst b/doc/userdoc/devdoc/sli_docs/objects-and-data-types.rst similarity index 100% rename from doc/userdoc/sli_docs/objects-and-data-types.rst rename to doc/userdoc/devdoc/sli_docs/objects-and-data-types.rst diff --git a/doc/userdoc/sli_docs/programming-in-sli.rst 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b/doc/userdoc/devdoc/workflows/ci.rst similarity index 100% rename from doc/userdoc/contribute/ci.rst rename to doc/userdoc/devdoc/workflows/ci.rst diff --git a/doc/userdoc/contribute/development_workflow.rst b/doc/userdoc/devdoc/workflows/development_workflow.rst similarity index 100% rename from doc/userdoc/contribute/development_workflow.rst rename to doc/userdoc/devdoc/workflows/development_workflow.rst diff --git a/doc/userdoc/documentation_workflow/developer_documentation_workflow.rst b/doc/userdoc/devdoc/workflows/documentation_workflow/developer_documentation_workflow.rst similarity index 100% rename from doc/userdoc/documentation_workflow/developer_documentation_workflow.rst rename to doc/userdoc/devdoc/workflows/documentation_workflow/developer_documentation_workflow.rst diff --git a/doc/userdoc/documentation_workflow/index.rst b/doc/userdoc/devdoc/workflows/documentation_workflow/index.rst similarity index 100% rename from doc/userdoc/documentation_workflow/index.rst rename to doc/userdoc/devdoc/workflows/documentation_workflow/index.rst diff --git a/doc/userdoc/documentation_workflow/user_documentation_workflow.rst b/doc/userdoc/devdoc/workflows/documentation_workflow/user_documentation_workflow.rst similarity index 100% rename from doc/userdoc/documentation_workflow/user_documentation_workflow.rst rename to doc/userdoc/devdoc/workflows/documentation_workflow/user_documentation_workflow.rst diff --git a/doc/userdoc/contribute/nest_with_ides.rst b/doc/userdoc/devdoc/workflows/nest_with_ides.rst similarity index 100% rename from doc/userdoc/contribute/nest_with_ides.rst rename to doc/userdoc/devdoc/workflows/nest_with_ides.rst diff --git a/doc/userdoc/developer_space.rst b/doc/userdoc/developer_space.rst deleted file mode 100644 index ded546f363..0000000000 --- a/doc/userdoc/developer_space.rst +++ /dev/null @@ -1,41 +0,0 @@ -Developer space -=============== - -Here is all documentation pertaining to the development of NEST. -It is documentation for anyone needing to touch the code or documentation (also includes SLI, since it is more complex -and likely used by developers or very advanced users). - - -* install and configure for developers - -* Workflows - - * documentation workflows - * git workflows - * pull request process contributor - * pull request process reviewer - * release workflow - * Working with IDEs - -* templates - - * pynest example - * pynest api - * PR template - -* styleguide and rules - - * code guidelines - * comments and docstring guidlines - * user level docs guide - * guidelines writing tests, benchmarks etc - -* doxygen - - * Doxyfile - * output of doxygen - -* SLI documentation - - * help generator - * guides . . . From bb3fff4efb827764444fe08fca65530cd1d4dec8 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 1 Feb 2022 21:36:24 +0100 Subject: [PATCH 13/43] fix broken link --- doc/userdoc/related_projects.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/userdoc/related_projects.rst b/doc/userdoc/related_projects.rst index a76f6c8ea1..e2c7bf7650 100644 --- a/doc/userdoc/related_projects.rst +++ b/doc/userdoc/related_projects.rst @@ -95,4 +95,4 @@ ConnPlotter The ConnPlotter package allows you to plot connection matrices from NEST. -* :ref: `Get started with ConnPlotter ` +* `Get started with ConnPlotter `_ From 70a7b6eac07a6d07025936f4d002dabdfb8b87ab Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 1 Feb 2022 21:36:41 +0100 Subject: [PATCH 14/43] add content to page --- doc/userdoc/models/models-main.rst | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/doc/userdoc/models/models-main.rst b/doc/userdoc/models/models-main.rst index bb405f5205..751a4e4228 100644 --- a/doc/userdoc/models/models-main.rst +++ b/doc/userdoc/models/models-main.rst @@ -1,2 +1,13 @@ Models in NEST ============== + + +NEST provides a ton of models! Textbook standards like integrate-and-fire and Hodgkin-Huxley type models are available +alongside high quality implementations of models published by the neuroscience community. + +* Discover :doc:`all the models in our directory ` + +Need to create your own? + +* Check out :doc:`NESTML `, a domain-specific language supporting neuron and synapse models without + any C++. From 4ab6ff7ad5ae08cee5a8a0243e30028d448d6c44 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 1 Feb 2022 21:36:51 +0100 Subject: [PATCH 15/43] add relatedt projects to toc --- doc/userdoc/contents.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index 2907c437a3..00af5a1e78 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -62,6 +62,7 @@ Table of Contents :maxdepth: 1 :caption: Community + related_projects Contribute Developer space News and updates From e2059d46ed2105ae8d6d4c39d9ee9458f11a85e1 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Thu, 3 Feb 2022 14:34:31 +0100 Subject: [PATCH 16/43] fix typo and add nest 2-3 ref guide --- doc/userdoc/contents.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index 00af5a1e78..e4bff67242 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -37,7 +37,7 @@ Table of Contents Neurons Synapses and connections Devices - Spatially-structured networks + Spatially-structured networks Simulation behavior Random numbers Built-in timers @@ -48,6 +48,7 @@ Table of Contents ref_material/pynest_apis Model directory + From NEST 2.x to 3.x Glossary .. toctree:: From d50d3f07c8f4957b18e4d38e538c0d5b3c89cd4d Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Mon, 7 Feb 2022 16:39:42 +0100 Subject: [PATCH 17/43] add reference to index pages and move glossary --- doc/userdoc/contents.rst | 2 +- doc/userdoc/coupling_nest_docs/index.rst | 4 +++- doc/userdoc/devdoc/index.rst | 2 ++ doc/userdoc/devdoc/sli_docs/index.rst | 2 ++ doc/userdoc/device_docs/index.rst | 2 ++ doc/userdoc/hpc_docs/index.rst | 2 ++ doc/userdoc/nest_behavior_docs/index.rst | 18 ++++++------------ doc/userdoc/network_docs/index.rst | 3 ++- doc/userdoc/neuron_docs/index.rst | 2 ++ doc/userdoc/{ => ref_material}/glossary.rst | 0 doc/userdoc/synapse_docs/index.rst | 2 ++ 11 files changed, 24 insertions(+), 15 deletions(-) rename doc/userdoc/{ => ref_material}/glossary.rst (100%) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index e4bff67242..9616651cfb 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -49,7 +49,7 @@ Table of Contents ref_material/pynest_apis Model directory From NEST 2.x to 3.x - Glossary + Glossary .. toctree:: :maxdepth: 1 diff --git a/doc/userdoc/coupling_nest_docs/index.rst b/doc/userdoc/coupling_nest_docs/index.rst index 17d66af74d..5145705cff 100644 --- a/doc/userdoc/coupling_nest_docs/index.rst +++ b/doc/userdoc/coupling_nest_docs/index.rst @@ -1,3 +1,5 @@ +.. _coupling_index: + Coupling NEST with other tools ============================== @@ -7,5 +9,5 @@ Communicate with other tools .. toctree:: :maxdepth: 1 - ../nest_server + nest_server using_nest_with_music diff --git a/doc/userdoc/devdoc/index.rst b/doc/userdoc/devdoc/index.rst index 2daaf7b098..fa54a4a9ed 100644 --- a/doc/userdoc/devdoc/index.rst +++ b/doc/userdoc/devdoc/index.rst @@ -1,3 +1,5 @@ +.. _developer_space: + Developer space =============== diff --git a/doc/userdoc/devdoc/sli_docs/index.rst b/doc/userdoc/devdoc/sli_docs/index.rst index c162685532..7aec67abbf 100644 --- a/doc/userdoc/devdoc/sli_docs/index.rst +++ b/doc/userdoc/devdoc/sli_docs/index.rst @@ -1,3 +1,5 @@ +.. _sli_doc: + SLI documentation ================= diff --git a/doc/userdoc/device_docs/index.rst b/doc/userdoc/device_docs/index.rst index 2bc2bb1cfe..2371536334 100644 --- a/doc/userdoc/device_docs/index.rst +++ b/doc/userdoc/device_docs/index.rst @@ -1,3 +1,5 @@ +.. _device_index: + All about devices in NEST ========================= diff --git a/doc/userdoc/hpc_docs/index.rst b/doc/userdoc/hpc_docs/index.rst index e53766c52c..1400b9de17 100644 --- a/doc/userdoc/hpc_docs/index.rst +++ b/doc/userdoc/hpc_docs/index.rst @@ -1,3 +1,5 @@ +.. _hpc_index: + All about high performance computing ==================================== diff --git a/doc/userdoc/nest_behavior_docs/index.rst b/doc/userdoc/nest_behavior_docs/index.rst index 2a89c33be2..eeef3fb870 100644 --- a/doc/userdoc/nest_behavior_docs/index.rst +++ b/doc/userdoc/nest_behavior_docs/index.rst @@ -1,18 +1,12 @@ +.. _behavior_index: + How NEST works ============== -* how to run simulations - -* built in timers - -* randomness in NEST - -* parallel computing > HPC - -* benchmarking > HPC - -* pinning threads > HPC - +.. toctree:: + built-in_timers + random_numbers + running_simulations diff --git a/doc/userdoc/network_docs/index.rst b/doc/userdoc/network_docs/index.rst index c7ec7f4356..14463befd1 100644 --- a/doc/userdoc/network_docs/index.rst +++ b/doc/userdoc/network_docs/index.rst @@ -1,3 +1,5 @@ +.. _network_index: + Guides to set up networks in NEST ================================= @@ -5,5 +7,4 @@ Guides to set up networks in NEST .. toctree:: :maxdepth: 1 - running_simulations spatially_structured_networks/spatially_structured_networks diff --git a/doc/userdoc/neuron_docs/index.rst b/doc/userdoc/neuron_docs/index.rst index 4718a6b6cc..7dd53e6c8f 100644 --- a/doc/userdoc/neuron_docs/index.rst +++ b/doc/userdoc/neuron_docs/index.rst @@ -1,3 +1,5 @@ +.. _neurons_index: + All about neurons in NEST ========================= diff --git a/doc/userdoc/glossary.rst b/doc/userdoc/ref_material/glossary.rst similarity index 100% rename from doc/userdoc/glossary.rst rename to doc/userdoc/ref_material/glossary.rst diff --git a/doc/userdoc/synapse_docs/index.rst b/doc/userdoc/synapse_docs/index.rst index 494f1e6c2f..d47d7a5219 100644 --- a/doc/userdoc/synapse_docs/index.rst +++ b/doc/userdoc/synapse_docs/index.rst @@ -1,3 +1,5 @@ +.. _synapse_index: + All about synapses and connections in NEST ========================================== From 8c7a355ef815711143a86de3811804e5ebdc4c0c Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 8 Mar 2022 11:56:33 +0100 Subject: [PATCH 18/43] rename folders, removing doc and rearrange toc files --- 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rename doc/userdoc/{synapse_docs => synapses}/simulations_with_gap_junctions.rst (100%) rename doc/userdoc/{synapse_docs => synapses}/weight_normalization.rst (100%) diff --git a/doc/userdoc/contents.rst b/doc/userdoc/contents.rst index 9616651cfb..9136935775 100644 --- a/doc/userdoc/contents.rst +++ b/doc/userdoc/contents.rst @@ -1,9 +1,6 @@ Table of Contents ================= -.. toctree:: - - index .. toctree:: :maxdepth: 1 @@ -13,34 +10,23 @@ Table of Contents tutorials/index PyNEST example scripts -.. toctree:: - :maxdepth: 1 - :caption: Release notes - - Release notes - - -.. toctree:: - :maxdepth: 1 - :caption: Specialized setup of NEST - - Connect to other tools - HPC optimization - Benchmarking - .. toctree:: :maxdepth: 1 :caption: Understand how NEST works NEST models - Neurons - Synapses and connections - Devices - Spatially-structured networks - Simulation behavior - Random numbers - Built-in timers + Neurons + Synapses and connections + Devices + Spatially-structured networks + Simulation behavior + Random numbers + Built-in timers + Connect to other tools + HPC optimization + Benchmarking + .. toctree:: :maxdepth: 1 @@ -53,19 +39,21 @@ Table of Contents .. toctree:: :maxdepth: 1 - :caption: Get help + :caption: Release notes + + Release notes - troubleshooting - Command line help - Contact us .. toctree:: :maxdepth: 1 :caption: Community + troubleshooting + Command line help + Contact us related_projects - Contribute - Developer space + Contribute + Developer space News and updates Publications NEST Initiative diff --git a/doc/userdoc/coupling_nest_docs/index.rst b/doc/userdoc/coupling_nest/index.rst similarity index 100% rename from doc/userdoc/coupling_nest_docs/index.rst rename to doc/userdoc/coupling_nest/index.rst diff --git a/doc/userdoc/devdoc/contribute.rst b/doc/userdoc/developer_space/contribute.rst similarity index 100% rename from doc/userdoc/devdoc/contribute.rst rename to doc/userdoc/developer_space/contribute.rst diff --git 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rename doc/{userdoc => }/tutorials/videos/index.rst (100%) rename doc/{userdoc => }/tutorials/videos/one_neuron.rst (100%) delete mode 100644 doc/userdoc/models/models-main.rst delete mode 100644 doc/userdoc/models/models-toc.rst diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 2ad7d764b1..727e437508 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -90,8 +90,8 @@ else () set( OUT_OF_TREE_BUILD "True" ) endif () -set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc/userdoc" ) -set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc/userdoc" ) +set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc" ) +set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc" ) add_custom_target( html COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}" || true diff --git a/doc/userdoc/_ext/HoverXTooltip.py b/doc/_ext/HoverXTooltip.py similarity index 98% rename from doc/userdoc/_ext/HoverXTooltip.py rename to doc/_ext/HoverXTooltip.py index 0bb5400ff7..03ceb5b584 100644 --- a/doc/userdoc/_ext/HoverXTooltip.py +++ b/doc/_ext/HoverXTooltip.py @@ -146,7 +146,7 @@ def role(name, rawtext, text, lineno, inliner, options={}, content=[]): refuri = (f'/en/{branch_name}/glossary.html#term-{term}') # for local builds else: - refuri = base_url.split('userdoc')[0] + f'userdoc/html/glossary.html#term-{term}' + refuri = base_url.split('doc')[0] + f'html/glossary.html#term-{term}' # the tag in which the term and description is defined. ref_tag = "`_. The NEST simulator documentation lives alongside its code. It is -contained in the ``doc/userdoc`` directory within the `NEST source +contained in the ``doc/`` directory within the `NEST source code repository `_ on GitHub. We work with `GitHub `_ as a web-based hosting @@ -97,11 +97,11 @@ directory where you ran ``cmake``) make html -3. Preview files. They are located in ``doc/userdoc/html`` +3. Preview files. They are located in ``doc/html`` .. code-block:: bash - browser doc/userdoc/html/index.html + browser doc/html/index.html To install the documentation under ```` along with the rest of NEST, the ``make html`` command can be followed by @@ -122,10 +122,10 @@ Editing and creating pages To edit existing `reStructuredText `_ files or to create new ones, follow the steps below: -1. You can edit and/or add ``.rst`` files in the ``doc/userdoc`` directory using your +1. You can edit and/or add ``.rst`` files in the ``doc`` directory using your editor of choice. -2. If you create a new page, open ``contents.rst`` in the ``doc/userdoc`` directory +2. If you create a new page, open ``contents.rst`` in the ``doc`` directory and add the file name under ``.. toctree::``. This will ensure it appears on the NEST simulator documentation's table of contents. diff --git a/doc/userdoc/developer_space/workflows/nest_with_ides.rst b/doc/developer_space/workflows/nest_with_ides.rst similarity index 100% rename from doc/userdoc/developer_space/workflows/nest_with_ides.rst rename to doc/developer_space/workflows/nest_with_ides.rst diff --git a/doc/userdoc/devices/index.rst b/doc/devices/index.rst similarity index 100% rename from doc/userdoc/devices/index.rst rename to doc/devices/index.rst diff --git a/doc/userdoc/devices/record_from_simulations.rst b/doc/devices/record_from_simulations.rst similarity index 100% rename from doc/userdoc/devices/record_from_simulations.rst rename to doc/devices/record_from_simulations.rst diff --git a/doc/userdoc/devices/stimulate_the_network.rst b/doc/devices/stimulate_the_network.rst similarity index 100% rename from doc/userdoc/devices/stimulate_the_network.rst rename to doc/devices/stimulate_the_network.rst diff --git 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doc/userdoc/tutorials/videos/index.rst rename to doc/tutorials/videos/index.rst diff --git a/doc/userdoc/tutorials/videos/one_neuron.rst b/doc/tutorials/videos/one_neuron.rst similarity index 100% rename from doc/userdoc/tutorials/videos/one_neuron.rst rename to doc/tutorials/videos/one_neuron.rst diff --git a/doc/userdoc/models/models-main.rst b/doc/userdoc/models/models-main.rst deleted file mode 100644 index 751a4e4228..0000000000 --- a/doc/userdoc/models/models-main.rst +++ /dev/null @@ -1,13 +0,0 @@ -Models in NEST -============== - - -NEST provides a ton of models! Textbook standards like integrate-and-fire and Hodgkin-Huxley type models are available -alongside high quality implementations of models published by the neuroscience community. - -* Discover :doc:`all the models in our directory ` - -Need to create your own? - -* Check out :doc:`NESTML `, a domain-specific language supporting neuron and synapse models without - any C++. diff --git a/doc/userdoc/models/models-toc.rst b/doc/userdoc/models/models-toc.rst deleted file mode 100644 index bb7d77adc6..0000000000 --- a/doc/userdoc/models/models-toc.rst +++ /dev/null @@ -1,12 +0,0 @@ -Models contents -=============== - - -.. toctree:: - :maxdepth: 1 - :hidden: - -{% for item in nest_models %} - {{ item }} -{% endfor %} - From 36de29e23d9533affd2aaf379094b0fed1343f55 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 8 Mar 2022 12:34:27 +0100 Subject: [PATCH 21/43] update paths to remove userdoc --- CONTRIBUTING.md | 2 +- libnestutil/propagator_stability.h | 2 +- testsuite/pytests/test_aeif_data_lsodar.dat | 2 +- testsuite/pytests/test_aeif_lsodar.py | 2 +- testsuite/pytests/test_regression_issue-1034.py | 4 ++-- testsuite/pytests/test_siegert_neuron.py | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index bbb1fc1387..6faa0c6f5b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -58,7 +58,7 @@ We review each pull request according to our [code review guidelines](https://ne ## Submitting Changes -* Sign the [Contributor License Agreement](https://raw.githubusercontent.com/nest/nest-simulator/master/doc/userdoc/contribute/NEST_Contributor_Agreement.pdf). +* Sign the [Contributor License Agreement](https://raw.githubusercontent.com/nest/nest-simulator/master/doc/contribute/NEST_Contributor_Agreement.pdf). * Push your changes to a topic branch in your fork of the repository. * Submit a pull request to the [NEST repository](https://github.com/nest/nest-simulator). * If your pull request affects documented issues, [mention](https://github.com/blog/957-introducing-issue-mentions) them in the description. If it is solving an issue, you can [state this explicitly](https://help.github.com/articles/closing-issues-via-commit-messages/). diff --git a/libnestutil/propagator_stability.h b/libnestutil/propagator_stability.h index 7c3e8b634a..c2aa0d832f 100644 --- a/libnestutil/propagator_stability.h +++ b/libnestutil/propagator_stability.h @@ -24,7 +24,7 @@ #define PROPAGATOR_STABILITY_H // Propagators to handle similar tau_m and tau_syn_* time constants. -// For details, please see doc/userdoc/model_details/IAF_neurons_singularity.ipynb. +// For details, please see doc/model_details/IAF_neurons_singularity.ipynb. double propagator_31( double tau_syn, double tau, double C, double h ); double propagator_32( double tau_syn, double tau, double C, double h ); diff --git a/testsuite/pytests/test_aeif_data_lsodar.dat b/testsuite/pytests/test_aeif_data_lsodar.dat index 1007fdca5f..8f84540381 100644 --- a/testsuite/pytests/test_aeif_data_lsodar.dat +++ b/testsuite/pytests/test_aeif_data_lsodar.dat @@ -6,7 +6,7 @@ # This .dat file contains the recordings of the potential and of the adaptation # variable of an aeif neuron, simulated using the LSODAR solver, with the # implementation detailed in -# ``doc/userdoc/model_details/aeif_models_implementation.ipynb``. +# ``doc/model_details/aeif_models_implementation.ipynb``. # This data is used as reference for the aeif tests in ``test_aeif_lsodar.py``. # # Times V_m w diff --git a/testsuite/pytests/test_aeif_lsodar.py b/testsuite/pytests/test_aeif_lsodar.py index d384c2dca7..28f8c9cd52 100644 --- a/testsuite/pytests/test_aeif_lsodar.py +++ b/testsuite/pytests/test_aeif_lsodar.py @@ -33,7 +33,7 @@ """ Comparing the new implementations the aeif models to the reference solution obrained using the LSODAR solver (see -``doc/userdoc/model_details/aeif_models_implementation.ipynb``). Also asserting that +``doc/model_details/aeif_models_implementation.ipynb``). Also asserting that the ``Delta_T == 0.`` solution works by comparing the non-adaptive aeif to the iaf model. diff --git a/testsuite/pytests/test_regression_issue-1034.py b/testsuite/pytests/test_regression_issue-1034.py index 1957b58903..50705c31e9 100644 --- a/testsuite/pytests/test_regression_issue-1034.py +++ b/testsuite/pytests/test_regression_issue-1034.py @@ -19,7 +19,7 @@ # You should have received a copy of the GNU General Public License # along with NEST. If not, see . -# Please see `doc/userdoc/model_details/test_post_trace.ipynb` for a version of this +# Please see `doc/model_details/test_post_trace.ipynb` for a version of this # test that includes more documentation and plotting. @@ -35,7 +35,7 @@ class PostTraceTester: with reference values generated in Python. For more information, please see the Jupyter notebook in - `doc/userdoc/model_details/test_post_trace.ipynb`. + `doc/model_details/test_post_trace.ipynb`. ''' def __init__(self, pre_spike_times, post_spike_times, delay, resolution, diff --git a/testsuite/pytests/test_siegert_neuron.py b/testsuite/pytests/test_siegert_neuron.py index c3d1323e80..3780b60616 100644 --- a/testsuite/pytests/test_siegert_neuron.py +++ b/testsuite/pytests/test_siegert_neuron.py @@ -100,7 +100,7 @@ def simulate_fix_input_stats(self, mu, sigma): nest.Connect(self.multimeter, self.siegert_neuron) # set output statistics of noise generator - # - for dt_scaling factor see doc/userdoc/model_details/noise_generator.ipynb + # - for dt_scaling factor see doc/model_details/noise_generator.ipynb # - takes var(V) = sigma^2 / 2 into account lif_params = self.lif_params mV_to_pA = lif_params["C_m"] / lif_params["tau_m"] From 28d6ad71fc4ed20666d2b3ed4a34f976d7397140 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 8 Mar 2022 20:30:48 +0100 Subject: [PATCH 22/43] fix broken links in networks --- .../spatially_structured_networks.rst | 132 +++++++++--------- 1 file changed, 66 insertions(+), 66 deletions(-) diff --git a/doc/networks/spatially_structured_networks/spatially_structured_networks.rst b/doc/networks/spatially_structured_networks/spatially_structured_networks.rst index 505f2d70d2..12ac0db12e 100644 --- a/doc/networks/spatially_structured_networks/spatially_structured_networks.rst +++ b/doc/networks/spatially_structured_networks/spatially_structured_networks.rst @@ -72,13 +72,13 @@ A very simple example We create a first, grid-based simple NodeCollection with the following command: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer1 #} :end-before: #{ end #} .. _fig_layer1: -.. figure:: spatially_structured_networks/figures/layer1.png +.. figure:: figures/layer1.png :name: fig:layer1 Simple grid-based NodeCollection centered about the origin. Blue circles mark @@ -141,13 +141,13 @@ Grid-based layers have a default extent of :math:`1\times 1`. You can specify a different extent of a layer, i.e., its size in :math:`x`- and :math:`y`-direction by passing the ``extent`` argument to ``nest.spatial.grid()``: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer2 #} :end-before: #{ end #} .. _fig_layer2: -.. figure:: spatially_structured_networks/figures/layer2.png +.. figure:: figures/layer2.png :name: fig:layer2 Same layer as in :numref:`fig_layer1`, but with different extent. @@ -171,13 +171,13 @@ be changed by passing the ``center`` argument to ``nest.spatial.grid()``. The following code creates layers centered about :math:`(0,0)`, :math:`(-1,1)`, and :math:`(1.5,0.5)`, respectively: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer3 #} :end-before: #{ end #} .. _fig_layer3: -.. figure:: spatially_structured_networks/figures/layer3.png +.. figure:: figures/layer3.png :name: fig:layer3 Three layers centered, respectively, about :math:`(0,0)` (blue), @@ -217,13 +217,13 @@ about :math:`y=0`, we have :math:`c_y=0`. Thus, the center coordinates are :math:`(n_x d/2, 0)`. The layer is created with the following code and shown in :numref:`fig_layer3a`: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer3a #} :end-before: #{ end #} .. _fig_layer3a: -.. figure:: spatially_structured_networks/figures/layer3a.png +.. figure:: figures/layer3a.png :name: fig:layer3a NodeCollection with :math:`n_x=5` columns and :math:`n_y=3` rows, spacing @@ -243,13 +243,13 @@ parameter to ``nest.spatial.free()``. The following code creates a NodeCollectio extent :math:`1\times 1`, i.e., spanning the square :math:`[-0.5,0.5]\times[-0.5,0.5]`: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer4 #} :end-before: #{ end #} .. _fig_layer4: -.. figure:: spatially_structured_networks/figures/layer4.png +.. figure:: figures/layer4.png :name: fig:layer4 A free layer with 50 elements uniformly distributed in an extent of @@ -280,13 +280,13 @@ Note the following points: To create a spatially distributed NodeCollection from a list, do the following: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer4b #} :end-before: #{ end #} .. _fig_layer4b: -.. figure:: spatially_structured_networks/figures/layer4b.png +.. figure:: figures/layer4b.png :name: fig:layer4b A free layer with 3 elements freely distributed space. The extent is given by the gray lines. @@ -302,13 +302,13 @@ Although the term “layer” suggests a 2-dimensional structure, the layers in NEST may in fact be 3-dimensional. The example from the previous section may be easily extended by updating number of dimensions for the positions: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer4_3d #} :end-before: #{ end #} .. _fig_layer4_3d: -.. figure:: spatially_structured_networks/figures/layer4_3d.png +.. figure:: figures/layer4_3d.png :name: fig:layer4_3d A free 3D layer with 200 elements uniformly distributed in an extent @@ -318,13 +318,13 @@ Again it is also possible to specify a list of list to create nodes in a 3-dimen space. Another possibility is to create a 3D grid-layer, with 3 elements passed to the shape argument, ``shape=[nx, ny, nz]``: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer4_3d_b #} :end-before: #{ end #} .. _fig_layer4_3d_b: -.. figure:: spatially_structured_networks/figures/layer4_3d_b.png +.. figure:: figures/layer4_3d_b.png :name: fig:layer4_3d_b A grid 3D NodeCollection with 120 elements distributed on a grid with 4 elements in the x-direction, @@ -355,13 +355,13 @@ introduction of periodic boundary conditions. You specify periodic boundary conditions for a NodeCollection using the entry ``edge_wrap``: -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ player #} :end-before: #{ end #} .. _fig_player: -.. figure:: spatially_structured_networks/figures/player.png +.. figure:: figures/player.png :name: fig:player Top left: Layer with single row and five columns without periodic @@ -399,11 +399,11 @@ be of interest: properties of the NodeCollection (``l`` is the layer created at the beginning of this guide): -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer1s #} :end-before: #{ end #} -.. literalinclude:: spatially_structured_networks/scripts/layers.log +.. literalinclude:: scripts/layers.log :start-after: #{ layer1s.log #} :end-before: #{ end.log #} @@ -419,11 +419,11 @@ not change properties of the spatially distributed NodeCollection. :py:func:`.Connect` with spatial dependence, or visualization of layers) can only be used on NodeCollections created with spatial distribution. -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ layer1p #} :end-before: #{ end #} -.. literalinclude:: spatially_structured_networks/scripts/layers.log +.. literalinclude:: scripts/layers.log :start-after: #{ layer1p.log #} :end-before: #{ end.log #} @@ -539,13 +539,13 @@ targets. Here is a simple example, cf. :numref:`fig_conn1` -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn1 #} :end-before: #{ end #} .. _fig_conn1: -.. figure:: spatially_structured_networks/figures/conn1.png +.. figure:: figures/conn1.png :name: fig:conn1 Left: Minimal connection example from a layer onto itself using a @@ -625,7 +625,7 @@ Rectangular specified by its lower left and upper right corners, measured in the same unit as element coordinates. Example: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2r #} :end-before: #{ end #} @@ -633,7 +633,7 @@ Circular All nodes within a circle are connected. The area is specified by its radius. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2c #} :end-before: #{ end #} @@ -642,7 +642,7 @@ Doughnut nodes *on* the inner circle are not connected. The area is specified by the radii of the inner and outer circles. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2d #} :end-before: #{ end #} @@ -650,13 +650,13 @@ Elliptical All nodes within an ellipsis are connected. The area is specified by its major and minor axis. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2e #} :end-before: #{ end #} .. _fig_conn2_a: -.. figure:: spatially_structured_networks/figures/conn2_a.png +.. figure:: figures/conn2_a.png :name: fig:conn2_a Masks for 2D layers. For all mask types, the driver node is marked by @@ -672,25 +672,25 @@ the mask dictionary. The anchor is a 2D vector specifying the location of the mask center relative to the driver node, as in the following examples (cf. :numref:`fig_conn2_b`). -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2ro #} :end-before: #{ end #} -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2co #} :end-before: #{ end #} -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2do #} :end-before: #{ end #} -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2eo #} :end-before: #{ end #} .. _fig_conn2_b: -.. figure:: spatially_structured_networks/figures/conn2_b.png +.. figure:: figures/conn2_b.png :name: fig:conn2_b The same masks as in :numref:`fig_conn2_a`, but centered about @@ -703,17 +703,17 @@ add an ``'azimuth_angle'`` entry in the specific mask dictionary. The ``azimuth_angle`` is measured in degrees and is the rotational angle from the x-axis to the y-axis. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2rr #} :end-before: #{ end #} -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn2er #} :end-before: #{ end #} .. _fig_conn2_c: -.. figure:: spatially_structured_networks/figures/conn2_c.png +.. figure:: figures/conn2_c.png :name: fig:conn2_c Rotated rectangular and elliptical mask from :numref:`fig_conn2_a` and @@ -733,7 +733,7 @@ Box by its lower left and upper right corners, measured in the same unit as element coordinates. Example: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn_3d_a #} :end-before: #{ end #} @@ -741,7 +741,7 @@ Spherical All nodes within a sphere are connected. The area is specified by its radius. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn_3d_b #} :end-before: #{ end #} @@ -749,7 +749,7 @@ Ellipsoidal All nodes within an ellipsoid are connected. The area is specified by its major, minor, and polar axis. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn_3d_c #} :end-before: #{ end #} @@ -768,7 +768,7 @@ the (possibly rotated) x-axis is missing. .. _fig_conn_3d: -.. figure:: spatially_structured_networks/figures/conn_3d.png +.. figure:: figures/conn_3d.png :name: fig:conn3d Masks for 3D NodeCollections. For all mask types, the driver node is marked by @@ -784,7 +784,7 @@ these, you specify the size of the mask not by lower left and upper right corner coordinates, but give their size in x and y direction, as in this example: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn3 #} :end-before: #{ end #} @@ -794,13 +794,13 @@ grid index :math:`[0,0]`\ (see :ref:`2.1.1 `), is aligned with the driver node. You can change this alignment by specifying an *anchor* for the mask: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn3c #} :end-before: #{ end #} You can even place the anchor outside the mask: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn3x #} :end-before: #{ end #} @@ -808,7 +808,7 @@ The resulting connection patterns are shown in :numref:`fig_conn3`. .. _fig_conn3: -.. figure:: spatially_structured_networks/figures/conn3.png +.. figure:: figures/conn3.png :name: fig:conn3 Grid masks for connections between grid-based layers. Left: @@ -947,7 +947,7 @@ parameters drawing values from random distributions. .. _fig_conn4: -.. figure:: spatially_structured_networks/figures/conn4.png +.. figure:: figures/conn4.png :name: fig:conn4 Illustration of various connection probabilities. Top left: constant probability, @@ -961,7 +961,7 @@ Several examples follow. They are illustrated in :numref:`fig_conn4`. Constant Fixed connection probability: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn4cp #} :end-before: #{ end #} @@ -971,7 +971,7 @@ Gaussian probability is 1 for :math:`d=0` and falls off with a “standard deviation” of :math:`\sigma=1`: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn4g #} :end-before: #{ end #} @@ -981,7 +981,7 @@ Cut-off Gaussian .. TODO: Reference to full Parameter table with nest.logic.conditional(). -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn4cut #} :end-before: #{ end #} @@ -991,7 +991,7 @@ Cut-off Gaussian :math:`y`- directions. This probability depends on displacement, not only on distance: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn42d #} :end-before: #{ end #} @@ -1022,7 +1022,7 @@ entire NodeCollection and is centered about the driver node. Linear example - .. literalinclude:: spatially_structured_networks/scripts/connections.py + .. literalinclude:: scripts/connections.py :start-after: #{ conn5lin #} :end-before: #{ end #} @@ -1036,7 +1036,7 @@ Linear example Linear example with periodic boundary conditions - .. literalinclude:: spatially_structured_networks/scripts/connections.py + .. literalinclude:: scripts/connections.py :start-after: #{ conn5linpbc #} :end-before: #{ end #} @@ -1048,11 +1048,11 @@ Linear example with periodic boundary conditions Various spatially dependent distributions - .. literalinclude:: spatially_structured_networks/scripts/connections.py + .. literalinclude:: scripts/connections.py :start-after: #{ conn5exp #} :end-before: #{ end #} - .. literalinclude:: spatially_structured_networks/scripts/connections.py + .. literalinclude:: scripts/connections.py :start-after: #{ conn5gauss #} :end-before: #{ end #} @@ -1063,7 +1063,7 @@ Various spatially dependent distributions Randomized weights and delays - .. literalinclude:: spatially_structured_networks/scripts/connections.py + .. literalinclude:: scripts/connections.py :start-after: #{ conn5uniform #} :end-before: #{ end #} @@ -1073,7 +1073,7 @@ Randomized weights and delays .. _fig_conn5: -.. figure:: spatially_structured_networks/figures/conn5.png +.. figure:: figures/conn5.png :name: fig:conn5 Distance-dependent and randomized weights and delays. See text for @@ -1096,13 +1096,13 @@ linear (actually affine) with respect to the displacement between the nodes, of \ where :math:`d_x` and :math:`d_y` are the displacements between the source and target neuron on the x and y axis, respectively. The parameter is then simply: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn_param_design #} :end-before: #{ end #} This can be directly plugged into the :py:func:`.Connect` function: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn_param_design_ex #} :end-before: #{ end #} @@ -1202,13 +1202,13 @@ distance. For the connection probability and parameter values below we have The resulting distribution of distances between connected nodes is shown in :numref:`fig_conn6`. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn6 #} :end-before: #{ end #} .. _fig_conn6: -.. figure:: spatially_structured_networks/figures/conn6.png +.. figure:: figures/conn6.png :name: fig:conn6 Distribution of distances between source and target for a network of @@ -1229,7 +1229,7 @@ model in NEST, ``static_synapse``. You can specify a different model by adding a ``'synapse_model'`` entry to the synapse specification dictionary, as in this example: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn8 #} :end-before: #{ end #} @@ -1250,14 +1250,14 @@ needs to be specified and optionally also an anchor for shifting the center of the mask. As demonstrated in the following example, stimulation devices have to be connected as the source layer. -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn9 #} :end-before: #{ end #} While recording devices, on the other hand, have to be connected as the target layer (see also the following section): -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn10 #} :end-before: #{ end #} @@ -1269,7 +1269,7 @@ another NodeCollection with spatial extent. This is especially true for spike re create a single spike recorder and connect all neurons in the spatially distributed NodeCollection to that spike recorder: -.. literalinclude:: spatially_structured_networks/scripts/connections.py +.. literalinclude:: scripts/connections.py :start-after: #{ conn11 #} :end-before: #{ end #} @@ -1361,7 +1361,7 @@ NEST provides three functions to visualize networks: .. _fig_vislayer: -.. figure:: spatially_structured_networks/figures/vislayer.png +.. figure:: figures/vislayer.png :name: fig:vislayer :math:`21\times 21` grid with divergent Gaussian projections onto @@ -1375,7 +1375,7 @@ which connects to itself with Gaussian connections. The resulting graphics is shown in :numref:`fig_vislayer`. All elements and the targets of the center neuron are shown, as well as mask and connection probability. -.. literalinclude:: spatially_structured_networks/scripts/layers.py +.. literalinclude:: scripts/layers.py :start-after: #{ vislayer #} :end-before: #{ end #} From a96e174dfc32c8976626a224ed55801d3d772e23 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 8 Mar 2022 20:31:09 +0100 Subject: [PATCH 23/43] fix link for tooltip --- doc/_ext/HoverXTooltip.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/doc/_ext/HoverXTooltip.py b/doc/_ext/HoverXTooltip.py index 03ceb5b584..04b8b884db 100644 --- a/doc/_ext/HoverXTooltip.py +++ b/doc/_ext/HoverXTooltip.py @@ -143,10 +143,10 @@ def role(name, rawtext, text, lineno, inliner, options={}, content=[]): # for rtd builds if os.environ.get("READTHEDOCS") == "True": branch_name = base_url.split('/doc/')[0].split('/')[-1] - refuri = (f'/en/{branch_name}/glossary.html#term-{term}') + refuri = (f'/en/{branch_name}/ref_material/glossary.html#term-{term}') # for local builds else: - refuri = base_url.split('doc')[0] + f'html/glossary.html#term-{term}' + refuri = base_url.split('doc')[0] + f'doc/html/ref_material/glossary.html#term-{term}' # the tag in which the term and description is defined. ref_tag = " Date: Tue, 8 Mar 2022 20:35:33 +0100 Subject: [PATCH 24/43] get make html to work - cp source contents, only remove html directory from build, adjust slidocs --- doc/CMakeLists.txt | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 727e437508..035f9af1d9 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -35,13 +35,13 @@ if ( NOT CMAKE_CROSSCOMPILING ) install( CODE "execute_process( COMMAND ${Python_EXECUTABLE} -B generate_help.py \"${PROJECT_SOURCE_DIR}\" \"${PROJECT_BINARY_DIR}\" - WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/slihelp_generator\" + WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/developer_space/sli_docs/slihelp_generator\" )" ) # Copy the local doc/help directory to the global installation # directory for documentation. - install( DIRECTORY "${PROJECT_BINARY_DIR}/doc/help" + install( DIRECTORY "${PROJECT_BINARY_DIR}/doc/developer_space/sli_docs/help" DESTINATION "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}" OPTIONAL ) @@ -51,7 +51,7 @@ if ( NOT CMAKE_CROSSCOMPILING ) install( CODE "execute_process( COMMAND ${Python_EXECUTABLE} -B generate_helpindex.py \"${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}\" - WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/slihelp_generator\" + WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/developer_space/sli_docs/slihelp_generator\" )" ) @@ -89,13 +89,12 @@ if ( "${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}" ) else () set( OUT_OF_TREE_BUILD "True" ) endif () - set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc" ) set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc" ) add_custom_target( html - COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}" || true - COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && cp -r "${DOC_SOURCE_DIR}" "${DOC_BUILD_DIR}" || true + COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}/html" || true + COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && cp -r "${DOC_SOURCE_DIR}/." "${DOC_BUILD_DIR}" || true COMMAND NESTSRCDIR=${PROJECT_SOURCE_DIR} sphinx-build -b html "${DOC_BUILD_DIR}" "${DOC_BUILD_DIR}/html" COMMAND cp "${DOC_BUILD_DIR}/models/*.rst" "${DOC_BUILD_DIR}/html/models" COMMAND ${PYTHON_EXECUTABLE} "${DOC_BUILD_DIR}/resolve_includes.py" "${DOC_BUILD_DIR}/html/models" From 8d6c7f5ddaf5dea80a012b82a732389a95fcf7b9 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 8 Mar 2022 21:36:54 +0100 Subject: [PATCH 25/43] .readthedocs.yml --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 321833c33b..05f4671137 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -2,7 +2,7 @@ version: 2 sphinx: builder: html - configuration: doc/userdoc/conf.py + configuration: doc/conf.py python: version: 3.8 From 088e4a2d315734204cb86fabb3fea61ddc2f6cb2 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 8 Mar 2022 22:04:08 +0100 Subject: [PATCH 26/43] fix mssg --- doc/_ext/HoverXTooltip.py | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/_ext/HoverXTooltip.py b/doc/_ext/HoverXTooltip.py index 04b8b884db..760081152c 100644 --- a/doc/_ext/HoverXTooltip.py +++ b/doc/_ext/HoverXTooltip.py @@ -212,7 +212,6 @@ def get_desc_from_glossary(term): with open(str(doc_build_dir) + '/ref_material/glossary.rst') as f: file_content = f.read() - print("HERE IS FFFFFF FFFFFF!!!!!!!", f) # generate a list of lines from file content. raw_file_content = list(filter(None, file_content .split('Glossary')[1].splitlines(True))) From 66220f54dc7b0155cae6a14b2e7d57747ac7286a Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 9 Mar 2022 09:37:02 +0100 Subject: [PATCH 27/43] fix pep8 --- doc/_ext/HoverXTooltip.py | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/_ext/HoverXTooltip.py b/doc/_ext/HoverXTooltip.py index 760081152c..2d9023defb 100644 --- a/doc/_ext/HoverXTooltip.py +++ b/doc/_ext/HoverXTooltip.py @@ -216,7 +216,6 @@ def get_desc_from_glossary(term): raw_file_content = list(filter(None, file_content .split('Glossary')[1].splitlines(True))) - glossary_dict = {} # dictionary that holds terms and descriptions. for idx, line in enumerate(raw_file_content): # detect a term based on value of first column. 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=> userdoc}/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst (100%) rename doc/{ => userdoc}/tutorials/videos/index.rst (100%) rename doc/{ => userdoc}/tutorials/videos/one_neuron.rst (100%) diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 035f9af1d9..5f885fa3bd 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -89,8 +89,9 @@ if ( "${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}" ) else () set( OUT_OF_TREE_BUILD "True" ) endif () -set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc" ) -set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc" ) + +set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc/userdoc" ) +set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc/userdoc" ) add_custom_target( html COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}/html" || true diff --git a/doc/_ext/HoverXTooltip.py b/doc/userdoc/_ext/HoverXTooltip.py similarity index 98% rename from doc/_ext/HoverXTooltip.py rename to doc/userdoc/_ext/HoverXTooltip.py index 2d9023defb..300eaf3c06 100644 --- a/doc/_ext/HoverXTooltip.py +++ b/doc/userdoc/_ext/HoverXTooltip.py @@ -146,7 +146,7 @@ def role(name, rawtext, text, lineno, inliner, options={}, content=[]): refuri = (f'/en/{branch_name}/ref_material/glossary.html#term-{term}') # for local builds else: - refuri = base_url.split('doc')[0] + f'doc/html/ref_material/glossary.html#term-{term}' + refuri = base_url.split('userdoc')[0] + f'userdoc/html/glossary.html#term-{term}' # the tag in which the term and description is defined. ref_tag = "`_. The NEST simulator documentation lives alongside its code. It is -contained in the ``doc/`` directory within the `NEST source +contained in the ``doc/userdoc`` directory within the `NEST source code repository `_ on GitHub. We work with `GitHub `_ as a web-based hosting @@ -97,11 +97,11 @@ directory where you ran ``cmake``) make html -3. Preview files. They are located in ``doc/html`` +3. Preview files. They are located in ``doc/userdoc/html`` .. code-block:: bash - browser doc/html/index.html + browser doc/userdoc/html/index.html To install the documentation under ```` along with the rest of NEST, the ``make html`` command can be followed by @@ -122,10 +122,10 @@ Editing and creating pages To edit existing `reStructuredText `_ files or to create new ones, follow the steps below: -1. You can edit and/or add ``.rst`` files in the ``doc`` directory using your +1. You can edit and/or add ``.rst`` files in the ``doc/userdoc`` directory using your editor of choice. -2. If you create a new page, open ``contents.rst`` in the ``doc`` directory +2. If you create a new page, open ``contents.rst`` in the ``doc/userdoc`` directory and add the file name under ``.. toctree::``. 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Textbook standards like integrate-and-fire and Hodgkin-Huxley type models are available +alongside high quality implementations of models published by the neuroscience community. + +* Discover :doc:`all the models in our directory ` + +Need to create your own? + +* Check out :doc:`NESTML `, a domain-specific language supporting neuron and synapse models without + any C++. diff --git a/doc/userdoc/models/models-toc.rst b/doc/userdoc/models/models-toc.rst new file mode 100644 index 0000000000..bb7d77adc6 --- /dev/null +++ b/doc/userdoc/models/models-toc.rst @@ -0,0 +1,12 @@ +Models contents +=============== + + +.. toctree:: + :maxdepth: 1 + :hidden: + +{% for item in nest_models %} + {{ item }} +{% endfor %} + diff --git a/doc/nest_behavior/built-in_timers.rst b/doc/userdoc/nest_behavior/built-in_timers.rst similarity index 100% rename from doc/nest_behavior/built-in_timers.rst rename to doc/userdoc/nest_behavior/built-in_timers.rst diff --git a/doc/nest_behavior/index.rst 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doc/userdoc/tutorials/pynest_tutorial/part_1_neurons_and_simple_neural_networks.rst diff --git a/doc/tutorials/pynest_tutorial/part_2_populations_of_neurons.rst b/doc/userdoc/tutorials/pynest_tutorial/part_2_populations_of_neurons.rst similarity index 100% rename from doc/tutorials/pynest_tutorial/part_2_populations_of_neurons.rst rename to doc/userdoc/tutorials/pynest_tutorial/part_2_populations_of_neurons.rst diff --git a/doc/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.rst b/doc/userdoc/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.rst similarity index 100% rename from doc/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.rst rename to doc/userdoc/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.rst diff --git a/doc/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst b/doc/userdoc/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst similarity index 100% rename from doc/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst rename to doc/userdoc/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst diff --git a/doc/tutorials/videos/index.rst b/doc/userdoc/tutorials/videos/index.rst similarity index 100% rename from doc/tutorials/videos/index.rst rename to doc/userdoc/tutorials/videos/index.rst diff --git a/doc/tutorials/videos/one_neuron.rst b/doc/userdoc/tutorials/videos/one_neuron.rst similarity index 100% rename from doc/tutorials/videos/one_neuron.rst rename to doc/userdoc/tutorials/videos/one_neuron.rst From aa831fe65a0e59b1b274702b5394a4416975b0ca Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 9 Mar 2022 12:32:03 +0100 Subject: [PATCH 29/43] Revert "update paths to remove userdoc" This reverts commit 36de29e23d9533affd2aaf379094b0fed1343f55. --- CONTRIBUTING.md | 2 +- libnestutil/propagator_stability.h | 2 +- testsuite/pytests/test_aeif_data_lsodar.dat | 2 +- testsuite/pytests/test_aeif_lsodar.py | 2 +- testsuite/pytests/test_regression_issue-1034.py | 4 ++-- testsuite/pytests/test_siegert_neuron.py | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6faa0c6f5b..bbb1fc1387 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -58,7 +58,7 @@ We review each pull request according to our [code review guidelines](https://ne ## Submitting Changes -* Sign the [Contributor License Agreement](https://raw.githubusercontent.com/nest/nest-simulator/master/doc/contribute/NEST_Contributor_Agreement.pdf). +* Sign the [Contributor License Agreement](https://raw.githubusercontent.com/nest/nest-simulator/master/doc/userdoc/contribute/NEST_Contributor_Agreement.pdf). * Push your changes to a topic branch in your fork of the repository. * Submit a pull request to the [NEST repository](https://github.com/nest/nest-simulator). * If your pull request affects documented issues, [mention](https://github.com/blog/957-introducing-issue-mentions) them in the description. If it is solving an issue, you can [state this explicitly](https://help.github.com/articles/closing-issues-via-commit-messages/). diff --git a/libnestutil/propagator_stability.h b/libnestutil/propagator_stability.h index c2aa0d832f..7c3e8b634a 100644 --- a/libnestutil/propagator_stability.h +++ b/libnestutil/propagator_stability.h @@ -24,7 +24,7 @@ #define PROPAGATOR_STABILITY_H // Propagators to handle similar tau_m and tau_syn_* time constants. -// For details, please see doc/model_details/IAF_neurons_singularity.ipynb. +// For details, please see doc/userdoc/model_details/IAF_neurons_singularity.ipynb. double propagator_31( double tau_syn, double tau, double C, double h ); double propagator_32( double tau_syn, double tau, double C, double h ); diff --git a/testsuite/pytests/test_aeif_data_lsodar.dat b/testsuite/pytests/test_aeif_data_lsodar.dat index 8f84540381..1007fdca5f 100644 --- a/testsuite/pytests/test_aeif_data_lsodar.dat +++ b/testsuite/pytests/test_aeif_data_lsodar.dat @@ -6,7 +6,7 @@ # This .dat file contains the recordings of the potential and of the adaptation # variable of an aeif neuron, simulated using the LSODAR solver, with the # implementation detailed in -# ``doc/model_details/aeif_models_implementation.ipynb``. +# ``doc/userdoc/model_details/aeif_models_implementation.ipynb``. # This data is used as reference for the aeif tests in ``test_aeif_lsodar.py``. # # Times V_m w diff --git a/testsuite/pytests/test_aeif_lsodar.py b/testsuite/pytests/test_aeif_lsodar.py index 28f8c9cd52..d384c2dca7 100644 --- a/testsuite/pytests/test_aeif_lsodar.py +++ b/testsuite/pytests/test_aeif_lsodar.py @@ -33,7 +33,7 @@ """ Comparing the new implementations the aeif models to the reference solution obrained using the LSODAR solver (see -``doc/model_details/aeif_models_implementation.ipynb``). Also asserting that +``doc/userdoc/model_details/aeif_models_implementation.ipynb``). Also asserting that the ``Delta_T == 0.`` solution works by comparing the non-adaptive aeif to the iaf model. diff --git a/testsuite/pytests/test_regression_issue-1034.py b/testsuite/pytests/test_regression_issue-1034.py index 50705c31e9..1957b58903 100644 --- a/testsuite/pytests/test_regression_issue-1034.py +++ b/testsuite/pytests/test_regression_issue-1034.py @@ -19,7 +19,7 @@ # You should have received a copy of the GNU General Public License # along with NEST. If not, see . -# Please see `doc/model_details/test_post_trace.ipynb` for a version of this +# Please see `doc/userdoc/model_details/test_post_trace.ipynb` for a version of this # test that includes more documentation and plotting. @@ -35,7 +35,7 @@ class PostTraceTester: with reference values generated in Python. For more information, please see the Jupyter notebook in - `doc/model_details/test_post_trace.ipynb`. + `doc/userdoc/model_details/test_post_trace.ipynb`. ''' def __init__(self, pre_spike_times, post_spike_times, delay, resolution, diff --git a/testsuite/pytests/test_siegert_neuron.py b/testsuite/pytests/test_siegert_neuron.py index 3780b60616..c3d1323e80 100644 --- a/testsuite/pytests/test_siegert_neuron.py +++ b/testsuite/pytests/test_siegert_neuron.py @@ -100,7 +100,7 @@ def simulate_fix_input_stats(self, mu, sigma): nest.Connect(self.multimeter, self.siegert_neuron) # set output statistics of noise generator - # - for dt_scaling factor see doc/model_details/noise_generator.ipynb + # - for dt_scaling factor see doc/userdoc/model_details/noise_generator.ipynb # - takes var(V) = sigma^2 / 2 into account lif_params = self.lif_params mV_to_pA = lif_params["C_m"] / lif_params["tau_m"] From 6be27197c47e50e9f469c2804c2f44cae4eb5a63 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 9 Mar 2022 12:33:42 +0100 Subject: [PATCH 30/43] revert changes to CMakeLists --- doc/CMakeLists.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 5f885fa3bd..2ad7d764b1 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -35,13 +35,13 @@ if ( NOT CMAKE_CROSSCOMPILING ) install( CODE "execute_process( COMMAND ${Python_EXECUTABLE} -B generate_help.py \"${PROJECT_SOURCE_DIR}\" \"${PROJECT_BINARY_DIR}\" - WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/developer_space/sli_docs/slihelp_generator\" + WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/slihelp_generator\" )" ) # Copy the local doc/help directory to the global installation # directory for documentation. - install( DIRECTORY "${PROJECT_BINARY_DIR}/doc/developer_space/sli_docs/help" + install( DIRECTORY "${PROJECT_BINARY_DIR}/doc/help" DESTINATION "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}" OPTIONAL ) @@ -51,7 +51,7 @@ if ( NOT CMAKE_CROSSCOMPILING ) install( CODE "execute_process( COMMAND ${Python_EXECUTABLE} -B generate_helpindex.py \"${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}\" - WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/developer_space/sli_docs/slihelp_generator\" + WORKING_DIRECTORY \"${PROJECT_SOURCE_DIR}/doc/slihelp_generator\" )" ) @@ -94,8 +94,8 @@ set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc/userdoc" ) set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc/userdoc" ) add_custom_target( html - COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}/html" || true - COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && cp -r "${DOC_SOURCE_DIR}/." "${DOC_BUILD_DIR}" || true + COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}" || true + COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && cp -r "${DOC_SOURCE_DIR}" "${DOC_BUILD_DIR}" || true COMMAND NESTSRCDIR=${PROJECT_SOURCE_DIR} sphinx-build -b html "${DOC_BUILD_DIR}" "${DOC_BUILD_DIR}/html" COMMAND cp "${DOC_BUILD_DIR}/models/*.rst" "${DOC_BUILD_DIR}/html/models" COMMAND ${PYTHON_EXECUTABLE} "${DOC_BUILD_DIR}/resolve_includes.py" "${DOC_BUILD_DIR}/html/models" From e3acfc424b0c0de835b9ed5c97ab74fcf4de0b82 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 9 Mar 2022 12:36:49 +0100 Subject: [PATCH 31/43] update path yml --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 05f4671137..321833c33b 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -2,7 +2,7 @@ version: 2 sphinx: builder: html - configuration: doc/conf.py + configuration: doc/userdoc/conf.py python: version: 3.8 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b/doc/slihelp_generator/templates/sample-footer.tmpl similarity index 100% rename from doc/userdoc/developer_space/sli_docs/slihelp_generator/templates/sample-footer.tmpl rename to doc/slihelp_generator/templates/sample-footer.tmpl diff --git a/doc/userdoc/developer_space/sli_docs/slihelp_generator/templates/sample-header.tmpl b/doc/slihelp_generator/templates/sample-header.tmpl similarity index 100% rename from doc/userdoc/developer_space/sli_docs/slihelp_generator/templates/sample-header.tmpl rename to doc/slihelp_generator/templates/sample-header.tmpl diff --git a/doc/userdoc/developer_space/sli_docs/slihelp_generator/writers.py b/doc/slihelp_generator/writers.py similarity index 100% rename from doc/userdoc/developer_space/sli_docs/slihelp_generator/writers.py rename to doc/slihelp_generator/writers.py From 643055af2dc40f60b7fd97eb6af373b9d47c74a7 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 9 Mar 2022 13:00:55 +0100 Subject: [PATCH 33/43] rename userdoc to htmldoc 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htmldoc}/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.rst (100%) rename doc/{userdoc => htmldoc}/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst (100%) rename doc/{userdoc => htmldoc}/tutorials/videos/index.rst (100%) rename doc/{userdoc => htmldoc}/tutorials/videos/one_neuron.rst (100%) diff --git a/.readthedocs.yml b/.readthedocs.yml index 321833c33b..8dc98cd523 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -2,7 +2,7 @@ version: 2 sphinx: builder: html - configuration: doc/userdoc/conf.py + configuration: doc/htmldoc/conf.py python: version: 3.8 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index bbb1fc1387..96d4af0476 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -58,7 +58,7 @@ We review each pull request according to our [code review guidelines](https://ne ## Submitting Changes -* Sign the [Contributor License Agreement](https://raw.githubusercontent.com/nest/nest-simulator/master/doc/userdoc/contribute/NEST_Contributor_Agreement.pdf). +* Sign the [Contributor License Agreement](https://raw.githubusercontent.com/nest/nest-simulator/master/doc/htmldoc/contribute/NEST_Contributor_Agreement.pdf). * Push your changes to a topic branch in your fork of the repository. * Submit a pull request to the [NEST repository](https://github.com/nest/nest-simulator). * If your pull request affects documented issues, [mention](https://github.com/blog/957-introducing-issue-mentions) them in the description. If it is solving an issue, you can [state this explicitly](https://help.github.com/articles/closing-issues-via-commit-messages/). diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 2ad7d764b1..7123d1d7df 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -90,8 +90,8 @@ else () set( OUT_OF_TREE_BUILD "True" ) endif () -set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc/userdoc" ) -set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc/userdoc" ) +set( DOC_BUILD_DIR "${PROJECT_BINARY_DIR}/doc/htmldoc" ) +set( DOC_SOURCE_DIR "${PROJECT_SOURCE_DIR}/doc/htmldoc" ) add_custom_target( html COMMAND [ "${OUT_OF_TREE_BUILD}" = "True" ] && rm -rf "${DOC_BUILD_DIR}" || true diff --git a/doc/userdoc/_ext/HoverXTooltip.py b/doc/htmldoc/_ext/HoverXTooltip.py similarity index 100% rename from doc/userdoc/_ext/HoverXTooltip.py rename to doc/htmldoc/_ext/HoverXTooltip.py diff --git a/doc/userdoc/_ext/VersionSyncRole.py b/doc/htmldoc/_ext/VersionSyncRole.py similarity index 100% rename from doc/userdoc/_ext/VersionSyncRole.py rename to doc/htmldoc/_ext/VersionSyncRole.py diff --git a/doc/userdoc/_ext/versions.json b/doc/htmldoc/_ext/versions.json similarity index 100% rename from doc/userdoc/_ext/versions.json rename to doc/htmldoc/_ext/versions.json diff --git a/doc/userdoc/citing-nest.rst b/doc/htmldoc/citing-nest.rst similarity index 100% rename from doc/userdoc/citing-nest.rst rename to doc/htmldoc/citing-nest.rst diff --git a/doc/userdoc/colorize.rst b/doc/htmldoc/colorize.rst similarity index 100% rename from doc/userdoc/colorize.rst rename to doc/htmldoc/colorize.rst diff --git a/doc/userdoc/community.rst b/doc/htmldoc/community.rst similarity index 100% rename from doc/userdoc/community.rst rename to doc/htmldoc/community.rst diff --git a/doc/userdoc/conf.py b/doc/htmldoc/conf.py similarity index 98% rename from doc/userdoc/conf.py rename to doc/htmldoc/conf.py index 0ae6ca2ac7..2e6f087757 100644 --- a/doc/userdoc/conf.py +++ b/doc/htmldoc/conf.py @@ -44,9 +44,9 @@ if os.environ.get("READTHEDOCS") == "True": - doc_build_dir = source_dir / "doc/userdoc" + doc_build_dir = source_dir / "doc/htmldoc" else: - doc_build_dir = Path(os.environ["OLDPWD"]) / "doc/userdoc" + doc_build_dir = Path(os.environ["OLDPWD"]) / "doc/htmldoc" sys.path.append(os.path.abspath("./_ext")) diff --git a/doc/userdoc/contents.rst b/doc/htmldoc/contents.rst similarity index 100% rename from doc/userdoc/contents.rst rename to doc/htmldoc/contents.rst diff --git a/doc/userdoc/coupling_nest/index.rst b/doc/htmldoc/coupling_nest/index.rst similarity index 100% rename from doc/userdoc/coupling_nest/index.rst rename to doc/htmldoc/coupling_nest/index.rst diff --git a/doc/userdoc/developer_space/contribute.rst b/doc/htmldoc/developer_space/contribute.rst similarity index 100% rename from doc/userdoc/developer_space/contribute.rst rename to doc/htmldoc/developer_space/contribute.rst diff --git a/doc/userdoc/developer_space/guidelines/code_review_guidelines.rst 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similarity index 100% rename from doc/userdoc/developer_space/workflows/development_workflow.rst rename to doc/htmldoc/developer_space/workflows/development_workflow.rst diff --git a/doc/userdoc/developer_space/workflows/documentation_workflow/developer_documentation_workflow.rst b/doc/htmldoc/developer_space/workflows/documentation_workflow/developer_documentation_workflow.rst similarity index 100% rename from doc/userdoc/developer_space/workflows/documentation_workflow/developer_documentation_workflow.rst rename to doc/htmldoc/developer_space/workflows/documentation_workflow/developer_documentation_workflow.rst diff --git a/doc/userdoc/developer_space/workflows/documentation_workflow/index.rst b/doc/htmldoc/developer_space/workflows/documentation_workflow/index.rst similarity index 100% rename from doc/userdoc/developer_space/workflows/documentation_workflow/index.rst rename to doc/htmldoc/developer_space/workflows/documentation_workflow/index.rst diff --git a/doc/userdoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst b/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst similarity index 95% rename from doc/userdoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst rename to doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst index d232bca0df..708c404fbb 100644 --- a/doc/userdoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst +++ b/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst @@ -14,7 +14,7 @@ reference `_. The NEST simulator documentation lives alongside its code. It is -contained in the ``doc/userdoc`` directory within the `NEST source +contained in the ``doc/htmldoc`` directory within the `NEST source code repository `_ on GitHub. We work with `GitHub `_ as a web-based hosting @@ -97,11 +97,11 @@ directory where you ran ``cmake``) make html -3. Preview files. They are located in ``doc/userdoc/html`` +3. Preview files. They are located in ``doc/htmldoc/html`` .. code-block:: bash - browser doc/userdoc/html/index.html + browser doc/htmldoc/html/index.html To install the documentation under ```` along with the rest of NEST, the ``make html`` command can be followed by @@ -122,10 +122,10 @@ Editing and creating pages To edit existing `reStructuredText `_ files or to create new ones, follow the steps below: -1. You can edit and/or add ``.rst`` files in the ``doc/userdoc`` directory using your +1. You can edit and/or add ``.rst`` files in the ``doc/htmldoc`` directory using your editor of choice. -2. If you create a new page, open ``contents.rst`` in the ``doc/userdoc`` directory +2. If you create a new page, open ``contents.rst`` in the ``doc/htmldoc`` directory and add the file name under ``.. toctree::``. 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doc/htmldoc/tutorials/videos/one_neuron.rst diff --git a/libnestutil/propagator_stability.h b/libnestutil/propagator_stability.h index 7c3e8b634a..8ad7ae9840 100644 --- a/libnestutil/propagator_stability.h +++ b/libnestutil/propagator_stability.h @@ -24,7 +24,7 @@ #define PROPAGATOR_STABILITY_H // Propagators to handle similar tau_m and tau_syn_* time constants. -// For details, please see doc/userdoc/model_details/IAF_neurons_singularity.ipynb. +// For details, please see doc/htmldoc/model_details/IAF_neurons_singularity.ipynb. double propagator_31( double tau_syn, double tau, double C, double h ); double propagator_32( double tau_syn, double tau, double C, double h ); diff --git a/testsuite/pytests/test_aeif_data_lsodar.dat b/testsuite/pytests/test_aeif_data_lsodar.dat index 1007fdca5f..caeca7fc70 100644 --- a/testsuite/pytests/test_aeif_data_lsodar.dat +++ b/testsuite/pytests/test_aeif_data_lsodar.dat @@ -6,7 +6,7 @@ # This .dat file contains the recordings of the potential and of the adaptation # variable of an aeif neuron, simulated using the LSODAR solver, with the # implementation detailed in -# ``doc/userdoc/model_details/aeif_models_implementation.ipynb``. +# ``doc/htmldoc/model_details/aeif_models_implementation.ipynb``. # This data is used as reference for the aeif tests in ``test_aeif_lsodar.py``. # # Times V_m w diff --git a/testsuite/pytests/test_aeif_lsodar.py b/testsuite/pytests/test_aeif_lsodar.py index d384c2dca7..98d94d7fbf 100644 --- a/testsuite/pytests/test_aeif_lsodar.py +++ b/testsuite/pytests/test_aeif_lsodar.py @@ -33,7 +33,7 @@ """ Comparing the new implementations the aeif models to the reference solution obrained using the LSODAR solver (see -``doc/userdoc/model_details/aeif_models_implementation.ipynb``). Also asserting that +``doc/htmldoc/model_details/aeif_models_implementation.ipynb``). Also asserting that the ``Delta_T == 0.`` solution works by comparing the non-adaptive aeif to the iaf model. diff --git a/testsuite/pytests/test_regression_issue-1034.py b/testsuite/pytests/test_regression_issue-1034.py index 1957b58903..e4a7ff0451 100644 --- a/testsuite/pytests/test_regression_issue-1034.py +++ b/testsuite/pytests/test_regression_issue-1034.py @@ -19,7 +19,7 @@ # You should have received a copy of the GNU General Public License # along with NEST. If not, see . -# Please see `doc/userdoc/model_details/test_post_trace.ipynb` for a version of this +# Please see `doc/htmldoc/model_details/test_post_trace.ipynb` for a version of this # test that includes more documentation and plotting. @@ -35,7 +35,7 @@ class PostTraceTester: with reference values generated in Python. For more information, please see the Jupyter notebook in - `doc/userdoc/model_details/test_post_trace.ipynb`. + `doc/htmldoc/model_details/test_post_trace.ipynb`. ''' def __init__(self, pre_spike_times, post_spike_times, delay, resolution, diff --git a/testsuite/pytests/test_siegert_neuron.py b/testsuite/pytests/test_siegert_neuron.py index c3d1323e80..23a9582bce 100644 --- a/testsuite/pytests/test_siegert_neuron.py +++ b/testsuite/pytests/test_siegert_neuron.py @@ -100,7 +100,7 @@ def simulate_fix_input_stats(self, mu, sigma): nest.Connect(self.multimeter, self.siegert_neuron) # set output statistics of noise generator - # - for dt_scaling factor see doc/userdoc/model_details/noise_generator.ipynb + # - for dt_scaling factor see doc/htmldoc/model_details/noise_generator.ipynb # - takes var(V) = sigma^2 / 2 into account lif_params = self.lif_params mV_to_pA = lif_params["C_m"] / lif_params["tau_m"] From fdddae526e162ee3a9a9f225f788d41bc5f5ebe8 Mon Sep 17 00:00:00 2001 From: jessica-mitchell Date: Mon, 14 Mar 2022 10:01:19 +0100 Subject: [PATCH 34/43] Update doc/htmldoc/models/models-main.rst Co-authored-by: Pooja Babu <75320801+pnbabu@users.noreply.github.com> --- doc/htmldoc/models/models-main.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/htmldoc/models/models-main.rst b/doc/htmldoc/models/models-main.rst index 751a4e4228..d8fa3d5a6b 100644 --- a/doc/htmldoc/models/models-main.rst +++ b/doc/htmldoc/models/models-main.rst @@ -9,5 +9,4 @@ alongside high quality implementations of models published by the neuroscience c Need to create your own? -* Check out :doc:`NESTML `, a domain-specific language supporting neuron and synapse models without - any C++. +* Check out :doc:`NESTML `, a domain-specific language supporting neuron and synapse models with a code generation backend that generates model code in C++ for NEST. From 0fd9eeff59645a073d039e022d3f2043e620fcd3 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Mon, 14 Mar 2022 10:33:35 +0100 Subject: [PATCH 35/43] apply suggestions from review --- doc/htmldoc/contents.rst | 8 +--- doc/htmldoc/coupling_nest/index.rst | 2 - .../nest_server.rst | 0 .../using_nest_with_music.rst | 0 doc/htmldoc/networks/index.rst | 10 ----- .../spatially_structured_networks.rst | 43 +++++++++---------- doc/htmldoc/neurons/parametrization.rst | 14 +++--- doc/htmldoc/synapses/handling_connections.rst | 2 +- 8 files changed, 31 insertions(+), 48 deletions(-) rename doc/htmldoc/{nest_behavior => coupling_nest}/nest_server.rst (100%) rename doc/htmldoc/{nest_behavior => coupling_nest}/using_nest_with_music.rst (100%) delete mode 100644 doc/htmldoc/networks/index.rst rename doc/htmldoc/networks/{spatially_structured_networks => }/spatially_structured_networks.rst (97%) diff --git a/doc/htmldoc/contents.rst b/doc/htmldoc/contents.rst index 9136935775..a6b9d2b15b 100644 --- a/doc/htmldoc/contents.rst +++ b/doc/htmldoc/contents.rst @@ -19,11 +19,11 @@ Table of Contents Neurons Synapses and connections Devices - Spatially-structured networks + Spatially-structured networks Simulation behavior Random numbers Built-in timers - Connect to other tools + Connect to other tools HPC optimization Benchmarking @@ -57,8 +57,4 @@ Table of Contents News and updates Publications NEST Initiative - -.. toctree:: - :maxdepth: 1 - license diff --git a/doc/htmldoc/coupling_nest/index.rst b/doc/htmldoc/coupling_nest/index.rst index 5145705cff..d032c3d06f 100644 --- a/doc/htmldoc/coupling_nest/index.rst +++ b/doc/htmldoc/coupling_nest/index.rst @@ -3,8 +3,6 @@ Coupling NEST with other tools ============================== -Transmit data -Communicate with other tools .. toctree:: :maxdepth: 1 diff --git a/doc/htmldoc/nest_behavior/nest_server.rst b/doc/htmldoc/coupling_nest/nest_server.rst similarity index 100% rename from doc/htmldoc/nest_behavior/nest_server.rst rename to doc/htmldoc/coupling_nest/nest_server.rst diff --git a/doc/htmldoc/nest_behavior/using_nest_with_music.rst b/doc/htmldoc/coupling_nest/using_nest_with_music.rst similarity index 100% rename from doc/htmldoc/nest_behavior/using_nest_with_music.rst rename to doc/htmldoc/coupling_nest/using_nest_with_music.rst diff --git a/doc/htmldoc/networks/index.rst b/doc/htmldoc/networks/index.rst deleted file mode 100644 index 14463befd1..0000000000 --- a/doc/htmldoc/networks/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -.. _network_index: - -Guides to set up networks in NEST -================================= - - -.. toctree:: - :maxdepth: 1 - - spatially_structured_networks/spatially_structured_networks diff --git a/doc/htmldoc/networks/spatially_structured_networks/spatially_structured_networks.rst b/doc/htmldoc/networks/spatially_structured_networks.rst similarity index 97% rename from doc/htmldoc/networks/spatially_structured_networks/spatially_structured_networks.rst rename to doc/htmldoc/networks/spatially_structured_networks.rst index 12ac0db12e..5eca9415ef 100644 --- a/doc/htmldoc/networks/spatially_structured_networks/spatially_structured_networks.rst +++ b/doc/htmldoc/networks/spatially_structured_networks.rst @@ -78,7 +78,7 @@ We create a first, grid-based simple NodeCollection with the following command: .. _fig_layer1: -.. figure:: figures/layer1.png +.. figure:: spatially_structured_networks/figures/layer1.png :name: fig:layer1 Simple grid-based NodeCollection centered about the origin. Blue circles mark @@ -147,7 +147,7 @@ different extent of a layer, i.e., its size in :math:`x`- and .. _fig_layer2: -.. figure:: figures/layer2.png +.. figure:: spatially_structured_networks/figures/layer2.png :name: fig:layer2 Same layer as in :numref:`fig_layer1`, but with different extent. @@ -177,7 +177,7 @@ The following code creates layers centered about :math:`(0,0)`, .. _fig_layer3: -.. figure:: figures/layer3.png +.. figure:: spatially_structured_networks/figures/layer3.png :name: fig:layer3 Three layers centered, respectively, about :math:`(0,0)` (blue), @@ -223,7 +223,7 @@ and shown in :numref:`fig_layer3a`: .. _fig_layer3a: -.. figure:: figures/layer3a.png +.. figure:: spatially_structured_networks/figures/layer3a.png :name: fig:layer3a NodeCollection with :math:`n_x=5` columns and :math:`n_y=3` rows, spacing @@ -249,7 +249,7 @@ extent :math:`1\times 1`, i.e., spanning the square .. _fig_layer4: -.. figure:: figures/layer4.png +.. figure:: spatially_structured_networks/figures/layer4.png :name: fig:layer4 A free layer with 50 elements uniformly distributed in an extent of @@ -286,7 +286,7 @@ To create a spatially distributed NodeCollection from a list, do the following: .. _fig_layer4b: -.. figure:: figures/layer4b.png +.. figure:: spatially_structured_networks/figures/layer4b.png :name: fig:layer4b A free layer with 3 elements freely distributed space. The extent is given by the gray lines. @@ -308,7 +308,7 @@ section may be easily extended by updating number of dimensions for the position .. _fig_layer4_3d: -.. figure:: figures/layer4_3d.png +.. figure:: spatially_structured_networks/figures/layer4_3d.png :name: fig:layer4_3d A free 3D layer with 200 elements uniformly distributed in an extent @@ -324,7 +324,7 @@ the shape argument, ``shape=[nx, ny, nz]``: .. _fig_layer4_3d_b: -.. figure:: figures/layer4_3d_b.png +.. figure:: spatially_structured_networks/figures/layer4_3d_b.png :name: fig:layer4_3d_b A grid 3D NodeCollection with 120 elements distributed on a grid with 4 elements in the x-direction, @@ -361,7 +361,7 @@ the entry ``edge_wrap``: .. _fig_player: -.. figure:: figures/player.png +.. figure:: spatially_structured_networks/figures/player.png :name: fig:player Top left: Layer with single row and five columns without periodic @@ -545,7 +545,7 @@ Here is a simple example, cf. :numref:`fig_conn1` .. _fig_conn1: -.. figure:: figures/conn1.png +.. figure:: spatially_structured_networks/figures/conn1.png :name: fig:conn1 Left: Minimal connection example from a layer onto itself using a @@ -656,7 +656,7 @@ Elliptical .. _fig_conn2_a: -.. figure:: figures/conn2_a.png +.. figure:: spatially_structured_networks/figures/conn2_a.png :name: fig:conn2_a Masks for 2D layers. For all mask types, the driver node is marked by @@ -690,7 +690,7 @@ examples (cf. :numref:`fig_conn2_b`). .. _fig_conn2_b: -.. figure:: figures/conn2_b.png +.. figure:: spatially_structured_networks/figures/conn2_b.png :name: fig:conn2_b The same masks as in :numref:`fig_conn2_a`, but centered about @@ -713,7 +713,7 @@ from the x-axis to the y-axis. .. _fig_conn2_c: -.. figure:: figures/conn2_c.png +.. figure:: spatially_structured_networks/figures/conn2_c.png :name: fig:conn2_c Rotated rectangular and elliptical mask from :numref:`fig_conn2_a` and @@ -768,7 +768,7 @@ the (possibly rotated) x-axis is missing. .. _fig_conn_3d: -.. figure:: figures/conn_3d.png +.. figure:: spatially_structured_networks/figures/conn_3d.png :name: fig:conn3d Masks for 3D NodeCollections. For all mask types, the driver node is marked by @@ -808,7 +808,7 @@ The resulting connection patterns are shown in :numref:`fig_conn3`. .. _fig_conn3: -.. figure:: figures/conn3.png +.. figure:: spatially_structured_networks/figures/conn3.png :name: fig:conn3 Grid masks for connections between grid-based layers. Left: @@ -947,7 +947,7 @@ parameters drawing values from random distributions. .. _fig_conn4: -.. figure:: figures/conn4.png +.. figure:: spatially_structured_networks/figures/conn4.png :name: fig:conn4 Illustration of various connection probabilities. Top left: constant probability, @@ -1013,7 +1013,7 @@ passed along in a synapse dictionary to the ``Connect()`` call. Figure :numref:`fig_conn5` illustrates weights and delays generated using these -parameters. The code examples used to generate the figures are shown below. +parameters. The code examples used to generate the spatially_structured_networks/figures are shown below. All examples use a spatially distributed NodeCollection of 51 nodes placed on a line; the line is centered about :math:`(25,0)`, so that the leftmost node has coordinates :math:`(0,0)`. The distance @@ -1073,7 +1073,7 @@ Randomized weights and delays .. _fig_conn5: -.. figure:: figures/conn5.png +.. figure:: spatially_structured_networks/figures/conn5.png :name: fig:conn5 Distance-dependent and randomized weights and delays. See text for @@ -1208,7 +1208,7 @@ The resulting distribution of distances between connected nodes is shown in .. _fig_conn6: -.. figure:: figures/conn6.png +.. figure:: spatially_structured_networks/figures/conn6.png :name: fig:conn6 Distribution of distances between source and target for a network of @@ -1361,7 +1361,7 @@ NEST provides three functions to visualize networks: .. _fig_vislayer: -.. figure:: figures/vislayer.png +.. figure:: spatially_structured_networks/figures/vislayer.png :name: fig:vislayer :math:`21\times 21` grid with divergent Gaussian projections onto @@ -1454,8 +1454,7 @@ Adding masks in a module If using parameters to define a connection boundary is not efficient enough, or if you need more flexibility in defining the mask, you can add a custom mask, written in C++, and add it to NEST via an extension module. For more information -on writing such modules, see the -`NEST extension module repository `_. +on writing such modules, see the :doc:`NEST extension module repository `. To add a mask, a subclass of ``nest::Mask`` must be defined, where ``D`` is the dimension (2 or 3). In this case we will define a 2-dimensional diff --git a/doc/htmldoc/neurons/parametrization.rst b/doc/htmldoc/neurons/parametrization.rst index b5266c2c20..bf8648dd1e 100644 --- a/doc/htmldoc/neurons/parametrization.rst +++ b/doc/htmldoc/neurons/parametrization.rst @@ -74,7 +74,7 @@ distribution. ax[0].set_ylabel('V_m'); -.. image:: ../../../static/img/NEST3_13_0.png +.. image:: ../static/img/NEST3_13_0.png .. _spatial_ex: @@ -108,7 +108,7 @@ To create spatially distributed nodes (see :ref:`spatial_networks` for more), us grid_nodes = nest.Create('iaf_psc_alpha', positions=nest.spatial.grid(shape=[10, 8])) nest.PlotLayer(grid_nodes); -.. image:: ../../../static/img/NEST3_23_0.png +.. image:: ../static/img/NEST3_23_0.png :width: 500px .. code-block:: ipython @@ -118,7 +118,7 @@ To create spatially distributed nodes (see :ref:`spatial_networks` for more), us num_dimensions=2)) nest.PlotLayer(free_nodes); -.. image:: ../../../static/img/NEST3_24_0.png +.. image:: ../static/img/NEST3_24_0.png :width: 500px After you have created your spatially distributed nodes, you can use the `spatial` property to set @@ -178,7 +178,7 @@ node or connection parameters. ax.set_xlabel('Node position on x-axis') ax.set_ylabel('V_m'); - .. image:: ../../../static/img/NEST3_25_0.png + .. image:: ../static/img/NEST3_25_0.png @@ -257,7 +257,7 @@ parameter: ax.set_xlabel('Target NodeID') ax.set_ylabel('Num. connections'); -.. image:: ../../../static/img/NEST3_34_0.png +.. image:: ../static/img/NEST3_34_0.png @@ -309,7 +309,7 @@ given as argument. -.. image:: ../../../static/img/NEST3_27_0.png +.. image:: ../static/img/NEST3_27_0.png .. _logic: @@ -401,7 +401,7 @@ statement. Three arguments are required: -.. image:: ../../../static/img/NEST3_26_0.png +.. image:: ../static/img/NEST3_26_0.png .. _compare_ex: diff --git a/doc/htmldoc/synapses/handling_connections.rst b/doc/htmldoc/synapses/handling_connections.rst index 4eaa7acb44..2e3bf1c8af 100644 --- a/doc/htmldoc/synapses/handling_connections.rst +++ b/doc/htmldoc/synapses/handling_connections.rst @@ -34,7 +34,7 @@ as NodeCollections. .. seealso:: - You can find a :doc:`full SynapseCollection example <../../../auto_examples/synapsecollection>` on our example + You can find a :doc:`full SynapseCollection example <../../auto_examples/synapsecollection>` on our example network page. Printing From f5094823bd1db465acc8c1d0383149d51864ade1 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Mon, 14 Mar 2022 11:28:03 +0100 Subject: [PATCH 36/43] fix sli docs index --- doc/htmldoc/developer_space/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/htmldoc/developer_space/index.rst b/doc/htmldoc/developer_space/index.rst index fa54a4a9ed..6351c639fd 100644 --- a/doc/htmldoc/developer_space/index.rst +++ b/doc/htmldoc/developer_space/index.rst @@ -44,7 +44,7 @@ and likely used by developers or very advanced users). :caption: SLI docs :glob: - sli_docs/* + sli_docs/index .. toctree:: :maxdepth: 1 From 11d635adfb5e30237c9554fff442d86fbd3be851 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 15 Mar 2022 18:28:55 +0100 Subject: [PATCH 37/43] apply suggestions from code review --- doc/htmldoc/citing-nest.rst | 2 -- doc/htmldoc/community.rst | 26 ++++++------------- doc/htmldoc/connect_nest/index.rst | 11 ++++++++ .../nest_server.rst | 0 .../using_nest_with_music.rst | 0 doc/htmldoc/contents.rst | 22 +++++++--------- doc/htmldoc/coupling_nest/index.rst | 11 -------- doc/htmldoc/developer_space/contribute.rst | 2 ++ .../nest_behavior/running_simulations.rst | 4 +-- 9 files changed, 32 insertions(+), 46 deletions(-) create mode 100644 doc/htmldoc/connect_nest/index.rst rename doc/htmldoc/{coupling_nest => connect_nest}/nest_server.rst (100%) rename doc/htmldoc/{coupling_nest => connect_nest}/using_nest_with_music.rst (100%) delete mode 100644 doc/htmldoc/coupling_nest/index.rst diff --git a/doc/htmldoc/citing-nest.rst b/doc/htmldoc/citing-nest.rst index a1dda3f985..51ddbae390 100644 --- a/doc/htmldoc/citing-nest.rst +++ b/doc/htmldoc/citing-nest.rst @@ -1,5 +1,3 @@ -:orphan: - .. _cite_nest: Cite NEST diff --git a/doc/htmldoc/community.rst b/doc/htmldoc/community.rst index c46c8da652..ef85860b26 100644 --- a/doc/htmldoc/community.rst +++ b/doc/htmldoc/community.rst @@ -1,7 +1,7 @@ .. _community: -NEST Community -============== +Contact us +========== Mailing list ------------ @@ -16,6 +16,12 @@ By subscribing to the mailing list you will also get notified of all NEST relate Before submitting a question, please take a look at our :ref:`guidelines for the NEST mailing list `. +Submit an issue or pull request on Github +----------------------------------------- + +You can :ref:`issues` on Github or contribute to the code or documentation. See our :ref:`contriute` page for +details. + Open video conference --------------------- @@ -25,20 +31,4 @@ This is an opportunity to have discussions in real time with developers. Information for dates and how to join can be found on `our GitHub wiki `_ -Publications using NEST ------------------------ - -We have compiled a `list of NEST-related peer-reviewed publications `_ that -we update regularly. - -If you have used NEST in your research, let us know! -Don't forget to :ref:`cite NEST ` in your work. - -Have a talk or poster where you used NEST? `Download our logo `_! - -Become a NEST member --------------------- - -If you would like to be actively involved in the NEST Initiative and support its -goals, please see our `member page `_. diff --git a/doc/htmldoc/connect_nest/index.rst b/doc/htmldoc/connect_nest/index.rst new file mode 100644 index 0000000000..b8931a01ed --- /dev/null +++ b/doc/htmldoc/connect_nest/index.rst @@ -0,0 +1,11 @@ +.. _connect_index: + +Connect NEST with other tools +============================= + + +.. toctree:: + :maxdepth: 1 + + nest_server + using_nest_with_music diff --git a/doc/htmldoc/coupling_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst similarity index 100% rename from doc/htmldoc/coupling_nest/nest_server.rst rename to doc/htmldoc/connect_nest/nest_server.rst diff --git a/doc/htmldoc/coupling_nest/using_nest_with_music.rst b/doc/htmldoc/connect_nest/using_nest_with_music.rst similarity index 100% rename from doc/htmldoc/coupling_nest/using_nest_with_music.rst rename to doc/htmldoc/connect_nest/using_nest_with_music.rst diff --git a/doc/htmldoc/contents.rst b/doc/htmldoc/contents.rst index a6b9d2b15b..da24b07952 100644 --- a/doc/htmldoc/contents.rst +++ b/doc/htmldoc/contents.rst @@ -21,10 +21,10 @@ Table of Contents Devices Spatially-structured networks Simulation behavior - Random numbers + Randomness in NEST Built-in timers - Connect to other tools - HPC optimization + Connect NEST with other tools + Parallel computing Benchmarking @@ -32,29 +32,25 @@ Table of Contents :maxdepth: 1 :caption: Reference material + Release notes ref_material/pynest_apis Model directory From NEST 2.x to 3.x Glossary -.. toctree:: - :maxdepth: 1 - :caption: Release notes - - Release notes - - .. toctree:: :maxdepth: 1 :caption: Community - troubleshooting - Command line help + Get help Contact us - related_projects Contribute + Cite NEST Developer space + related_projects News and updates Publications NEST Initiative license + + diff --git a/doc/htmldoc/coupling_nest/index.rst b/doc/htmldoc/coupling_nest/index.rst deleted file mode 100644 index d032c3d06f..0000000000 --- a/doc/htmldoc/coupling_nest/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -.. _coupling_index: - -Coupling NEST with other tools -============================== - - -.. toctree:: - :maxdepth: 1 - - nest_server - using_nest_with_music diff --git a/doc/htmldoc/developer_space/contribute.rst b/doc/htmldoc/developer_space/contribute.rst index 26d0de8e74..2814eb17b2 100644 --- a/doc/htmldoc/developer_space/contribute.rst +++ b/doc/htmldoc/developer_space/contribute.rst @@ -19,6 +19,8 @@ you need to send us a completed and signed :download:`NEST Contributor Agreement ` to transfer your copyright to the NEST Initiative before we can merge your pull request. +.. _issues: + Report bugs and request features -------------------------------- diff --git a/doc/htmldoc/nest_behavior/running_simulations.rst b/doc/htmldoc/nest_behavior/running_simulations.rst index b7697ced3d..af7ee87736 100644 --- a/doc/htmldoc/nest_behavior/running_simulations.rst +++ b/doc/htmldoc/nest_behavior/running_simulations.rst @@ -1,7 +1,7 @@ .. _run_simulations: -How to run simulations -====================== +Simulation behavior +=================== Time-driven and event-driven approaches --------------------------------------- From 84dbab161bbd6c5943e8de58883160d882297984 Mon Sep 17 00:00:00 2001 From: jessica-mitchell Date: Fri, 18 Mar 2022 07:48:48 +0100 Subject: [PATCH 38/43] Update doc/htmldoc/community.rst Co-authored-by: Pooja Babu <75320801+pnbabu@users.noreply.github.com> --- doc/htmldoc/community.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/htmldoc/community.rst b/doc/htmldoc/community.rst index ef85860b26..e155d92d89 100644 --- a/doc/htmldoc/community.rst +++ b/doc/htmldoc/community.rst @@ -19,7 +19,7 @@ Before submitting a question, please take a look at our :ref:`guidelines for the Submit an issue or pull request on Github ----------------------------------------- -You can :ref:`issues` on Github or contribute to the code or documentation. See our :ref:`contriute` page for +You can :ref:`issues` on Github or contribute to the code or documentation. See our :ref:`contribute` page for details. Open video conference From 225bd4e2ee6bf01a47b18b195a820e012c00acde Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 20 Apr 2022 10:42:29 +0200 Subject: [PATCH 39/43] apply suggestions from discussion, simplify toc --- doc/htmldoc/citing-nest.rst | 2 +- doc/htmldoc/community.rst | 22 +++++++-- doc/htmldoc/contents.rst | 47 ++----------------- doc/htmldoc/developer_space/contribute.rst | 5 +- .../guidelines/code_review_guidelines.rst | 2 +- .../guidelines/styleguide/styleguide.rst | 2 +- doc/htmldoc/developer_space/index.rst | 8 +--- doc/htmldoc/get-started_index.rst | 9 ++++ doc/htmldoc/getting_help.rst | 10 ++-- doc/htmldoc/understand_index.rst | 21 +++++++++ 10 files changed, 65 insertions(+), 63 deletions(-) create mode 100644 doc/htmldoc/get-started_index.rst create mode 100644 doc/htmldoc/understand_index.rst diff --git a/doc/htmldoc/citing-nest.rst b/doc/htmldoc/citing-nest.rst index 51ddbae390..9055fc270d 100644 --- a/doc/htmldoc/citing-nest.rst +++ b/doc/htmldoc/citing-nest.rst @@ -3,7 +3,7 @@ Cite NEST ========= -Please cite the version of NEST you used in your work. You can :ref:`let us know ` about your publications that used NEST, and we +Please cite the version of NEST you used in your work. You can :ref:`let us know ` about your publications that used NEST, and we will add them to our `publication list `_; this will help make them visible to potential readers. diff --git a/doc/htmldoc/community.rst b/doc/htmldoc/community.rst index e155d92d89..2e458a5b10 100644 --- a/doc/htmldoc/community.rst +++ b/doc/htmldoc/community.rst @@ -1,10 +1,24 @@ .. _community: +Community +========= + +.. toctree:: + :maxdepth: 1 + + News and updates + Publications + NEST Initiative + related_projects + citing-nest + +.. _contact_us: + Contact us -========== +---------- Mailing list ------------- +~~~~~~~~~~~~ The NEST users mailing list is intended to be a forum for questions on the usage of NEST, the exchange of code and general discussions about NEST. The philosophy @@ -17,13 +31,13 @@ By subscribing to the mailing list you will also get notified of all NEST relate Before submitting a question, please take a look at our :ref:`guidelines for the NEST mailing list `. Submit an issue or pull request on Github ------------------------------------------ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You can :ref:`issues` on Github or contribute to the code or documentation. See our :ref:`contribute` page for details. Open video conference ---------------------- +~~~~~~~~~~~~~~~~~~~~~ Every two weeks, we have an open video conference to discuss current issues and developments in NEST. We welcome users with questions regarding their implementations or issues they want help solving to join. diff --git a/doc/htmldoc/contents.rst b/doc/htmldoc/contents.rst index da24b07952..2a042c8633 100644 --- a/doc/htmldoc/contents.rst +++ b/doc/htmldoc/contents.rst @@ -4,53 +4,14 @@ Table of Contents .. toctree:: :maxdepth: 1 - :caption: Get started Install NEST - tutorials/index - PyNEST example scripts - - -.. toctree:: - :maxdepth: 1 - :caption: Understand how NEST works - - NEST models - Neurons - Synapses and connections - Devices - Spatially-structured networks - Simulation behavior - Randomness in NEST - Built-in timers - Connect NEST with other tools - Parallel computing - Benchmarking - - -.. toctree:: - :maxdepth: 1 - :caption: Reference material - - Release notes - ref_material/pynest_apis + Tutorials and examples + Understand how NEST works + API Model directory - From NEST 2.x to 3.x - Glossary - -.. toctree:: - :maxdepth: 1 - :caption: Community - Get help - Contact us Contribute - Cite NEST - Developer space - related_projects - News and updates - Publications - NEST Initiative + Community license - diff --git a/doc/htmldoc/developer_space/contribute.rst b/doc/htmldoc/developer_space/contribute.rst index 2814eb17b2..380524b665 100644 --- a/doc/htmldoc/developer_space/contribute.rst +++ b/doc/htmldoc/developer_space/contribute.rst @@ -72,6 +72,9 @@ See also https://github.com/nest/nest-extension-module for details about the gen Have a question? ---------------- -If you want to get in contact with us, see our :ref:`community` page for ways you can reach us. +If you want to get in contact with us, see our :ref:`contact_us` section for ways you can reach us. +.. note:: + + For all developer related topics see our :ref:`developer_space` diff --git a/doc/htmldoc/developer_space/guidelines/code_review_guidelines.rst b/doc/htmldoc/developer_space/guidelines/code_review_guidelines.rst index df2ea6a142..7184d9b201 100644 --- a/doc/htmldoc/developer_space/guidelines/code_review_guidelines.rst +++ b/doc/htmldoc/developer_space/guidelines/code_review_guidelines.rst @@ -11,7 +11,7 @@ stricter rules on code that ends up in the public repository. Following are rough guidelines for the code reviewers. These are not meant to prevent progress, but to keep up the code quality as the number of developers is growing. All of this is not set in stone and -can be discussed on the :ref:`NEST mailing lists `. +can be discussed on the :ref:`NEST mailing lists `. * In general, the rule is that each pull request needs an OK from the CI platform and at least two reviewers to be merged. diff --git a/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst b/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst index d7f4553789..06d111ccc9 100644 --- a/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst +++ b/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst @@ -72,7 +72,7 @@ references should be provided for clarity in introductory texts and the :ref:`gl If you have further questions about style rules not addressed here, use `the Microsoft style guide `_ as a resource -or ask on the :ref:`mailing list `. +or ask on the :ref:`mailing list `. How to phrase content in NEST ----------------------------- diff --git a/doc/htmldoc/developer_space/index.rst b/doc/htmldoc/developer_space/index.rst index 6351c639fd..270e856da3 100644 --- a/doc/htmldoc/developer_space/index.rst +++ b/doc/htmldoc/developer_space/index.rst @@ -4,8 +4,7 @@ Developer space =============== Here is all documentation pertaining to the development of NEST. -It is documentation for anyone needing to touch the code or documentation (also includes SLI, since it is more complex -and likely used by developers or very advanced users). +It is documentation for anyone needing to touch the code or documentation. .. toctree:: @@ -46,8 +45,3 @@ and likely used by developers or very advanced users). sli_docs/index -.. toctree:: - :maxdepth: 1 - :caption: Doxygen output - - doxygen/ diff --git a/doc/htmldoc/get-started_index.rst b/doc/htmldoc/get-started_index.rst new file mode 100644 index 0000000000..dbc362a006 --- /dev/null +++ b/doc/htmldoc/get-started_index.rst @@ -0,0 +1,9 @@ +Tutorials and examples +====================== + +.. toctree:: + :maxdepth: 1 + + tutorials/index + PyNEST example scripts + diff --git a/doc/htmldoc/getting_help.rst b/doc/htmldoc/getting_help.rst index 22e001c0c1..5413a96075 100644 --- a/doc/htmldoc/getting_help.rst +++ b/doc/htmldoc/getting_help.rst @@ -1,7 +1,7 @@ .. _getting_help: -Getting help -============ +Get help +======= Have a specific question or problem with NEST? ---------------------------------------------- @@ -10,10 +10,10 @@ Check out the :ref:`troubleshooting section ` for common issues. If your question is not on there, you are welcome to subscribe to our -:ref:`Mailing List ` and ask. +:ref:`Mailing List ` and ask. -Getting help on the command line interface ------------------------------------------- +Get help on the command line interface +-------------------------------------- * The :py:func:`.helpdesk` command will launch the documentation pages on your browser. diff --git a/doc/htmldoc/understand_index.rst b/doc/htmldoc/understand_index.rst new file mode 100644 index 0000000000..689ddabf85 --- /dev/null +++ b/doc/htmldoc/understand_index.rst @@ -0,0 +1,21 @@ +Understand how NEST works +========================= + + +.. toctree:: + :maxdepth: 1 + + From NEST 2.x to 3.x + NEST models + Neurons + Synapses and connections + Devices + Spatially-structured networks + Simulation behavior + Randomness in NEST + Built-in timers + Connect NEST with other tools + Parallel computing + Benchmarking + Release notes + Glossary From 26a240d7d6ab04efd664e33ad35e3cc5a1d9fb58 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Fri, 22 Apr 2022 09:09:53 +0200 Subject: [PATCH 40/43] pep8 --- pynest/examples/store_restore_network.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pynest/examples/store_restore_network.py b/pynest/examples/store_restore_network.py index a3cf5a7aca..9de07b0fc9 100644 --- a/pynest/examples/store_restore_network.py +++ b/pynest/examples/store_restore_network.py @@ -72,6 +72,7 @@ # input. Excitatory connections are plastic (STDP). Spike activity of # the excitatory population is recorded. + class EINetwork: """ A simple balanced random network with plastic excitatory synapses. From c754efdb85234d1a5d3774946a22530ffaf1e885 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 4 May 2022 14:00:29 +0200 Subject: [PATCH 41/43] apply suggestions from review --- doc/htmldoc/community.rst | 25 ++++++++++++------- doc/htmldoc/conf.py | 7 ++++-- doc/htmldoc/contents.rst | 17 ------------- .../user_documentation_workflow.rst | 2 +- doc/htmldoc/getting_help.rst | 8 +++--- doc/htmldoc/index.rst | 14 +++++++++++ doc/htmldoc/license.rst | 2 +- doc/htmldoc/understand_index.rst | 4 +-- 8 files changed, 43 insertions(+), 36 deletions(-) delete mode 100644 doc/htmldoc/contents.rst diff --git a/doc/htmldoc/community.rst b/doc/htmldoc/community.rst index 2e458a5b10..5438e7a871 100644 --- a/doc/htmldoc/community.rst +++ b/doc/htmldoc/community.rst @@ -3,15 +3,6 @@ Community ========= -.. toctree:: - :maxdepth: 1 - - News and updates - Publications - NEST Initiative - related_projects - citing-nest - .. _contact_us: Contact us @@ -30,6 +21,7 @@ By subscribing to the mailing list you will also get notified of all NEST relate Before submitting a question, please take a look at our :ref:`guidelines for the NEST mailing list `. + Submit an issue or pull request on Github ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46,3 +38,18 @@ This is an opportunity to have discussions in real time with developers. Information for dates and how to join can be found on `our GitHub wiki `_ +.. include:: getting_help.rst + +Explore the NEST ecosystem +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. toctree:: + :maxdepth: 1 + + News and updates + Publications + NEST Initiative + related_projects + citing-nest + + diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py index 2e6f087757..ab60eec068 100644 --- a/doc/htmldoc/conf.py +++ b/doc/htmldoc/conf.py @@ -51,7 +51,7 @@ sys.path.append(os.path.abspath("./_ext")) source_suffix = '.rst' -master_doc = 'contents' +master_doc = 'index' # Create the mockfile for extracting the PyNEST @@ -164,7 +164,10 @@ html_theme = 'sphinx_rtd_theme' html_logo = str(doc_build_dir / 'static/img/nest_logo.png') html_theme_options = {'logo_only': True, - 'display_version': True} + 'display_version': True, + 'style_external_links':True} + +logo_url: 'https://nest-simulator.com/documentation' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the diff --git a/doc/htmldoc/contents.rst b/doc/htmldoc/contents.rst deleted file mode 100644 index 2a042c8633..0000000000 --- a/doc/htmldoc/contents.rst +++ /dev/null @@ -1,17 +0,0 @@ -Table of Contents -================= - - -.. toctree:: - :maxdepth: 1 - - Install NEST - Tutorials and examples - Understand how NEST works - API - Model directory - Get help - Contribute - Community - license - diff --git a/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst b/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst index 708c404fbb..1790b73407 100644 --- a/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst +++ b/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst @@ -125,7 +125,7 @@ sphinx/rest_syntax.html>`_ files or to create new ones, follow the steps below: 1. You can edit and/or add ``.rst`` files in the ``doc/htmldoc`` directory using your editor of choice. -2. If you create a new page, open ``contents.rst`` in the ``doc/htmldoc`` directory +2. If you create a new page, open ``index.rst`` in the ``doc/htmldoc`` directory and add the file name under ``.. toctree::``. This will ensure it appears on the NEST simulator documentation's table of contents. diff --git a/doc/htmldoc/getting_help.rst b/doc/htmldoc/getting_help.rst index 5413a96075..0f7a5b952d 100644 --- a/doc/htmldoc/getting_help.rst +++ b/doc/htmldoc/getting_help.rst @@ -1,10 +1,10 @@ .. _getting_help: Get help -======= +-------- Have a specific question or problem with NEST? ----------------------------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Check out the :ref:`troubleshooting section ` for common issues. @@ -13,7 +13,7 @@ If your question is not on there, you are welcome to subscribe to our :ref:`Mailing List ` and ask. Get help on the command line interface --------------------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * The :py:func:`.helpdesk` command will launch the documentation pages on your browser. @@ -31,7 +31,7 @@ Get help on the command line interface nest.FunctionName? Model information ------------------ +~~~~~~~~~~~~~~~~~ * To get a list of available neuron models, use: diff --git a/doc/htmldoc/index.rst b/doc/htmldoc/index.rst index 799e66fa54..4d9ea09229 100644 --- a/doc/htmldoc/index.rst +++ b/doc/htmldoc/index.rst @@ -2,6 +2,20 @@ Welcome to the NEST simulator documentation! ******************************************** + +.. toctree:: + :maxdepth: 1 + :hidden: + + Install NEST + Tutorials and examples + Understand how NEST works + API + Model directory + Contribute + Community + license + In our :ref:`release notes `, you can find an overview of the newest changes and features for NEST 3.x. If you are transitioning from NEST 2.x to NEST 3.x, check out our :ref:`reference guide `. diff --git a/doc/htmldoc/license.rst b/doc/htmldoc/license.rst index cbaf8c2cc7..0775d14508 100644 --- a/doc/htmldoc/license.rst +++ b/doc/htmldoc/license.rst @@ -1,4 +1,4 @@ -.. _licesne: +.. _license: License ======= diff --git a/doc/htmldoc/understand_index.rst b/doc/htmldoc/understand_index.rst index 689ddabf85..baca22bf20 100644 --- a/doc/htmldoc/understand_index.rst +++ b/doc/htmldoc/understand_index.rst @@ -5,17 +5,17 @@ Understand how NEST works .. toctree:: :maxdepth: 1 - From NEST 2.x to 3.x - NEST models Neurons Synapses and connections Devices Spatially-structured networks + NEST models Simulation behavior Randomness in NEST Built-in timers Connect NEST with other tools Parallel computing Benchmarking + From NEST 2.x to 3.x Release notes Glossary From 38595a243ed0c15ff38d72f332e0c0208978606e Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 4 May 2022 14:07:20 +0200 Subject: [PATCH 42/43] pep8 --- doc/htmldoc/conf.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py index ab60eec068..c5097b9e0f 100644 --- a/doc/htmldoc/conf.py +++ b/doc/htmldoc/conf.py @@ -165,9 +165,7 @@ html_logo = str(doc_build_dir / 'static/img/nest_logo.png') html_theme_options = {'logo_only': True, 'display_version': True, - 'style_external_links':True} - -logo_url: 'https://nest-simulator.com/documentation' + 'style_external_links': True} # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -316,3 +314,4 @@ def copy_acknowledgments_file(src): copy_example_file(source_dir / "pynest/examples/Potjans_2014/microcircuit.png") copy_example_file(source_dir / "pynest/examples/Potjans_2014/README.rst") copy_example_file(source_dir / "pynest/examples/hpc_benchmark_connectivity.svg") + From c909ce41b2c7b05407a9279781b1e1bc5ee1fbf2 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 4 May 2022 19:31:53 +0200 Subject: [PATCH 43/43] pep8 --- doc/htmldoc/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py index c5097b9e0f..33a1ad0c5f 100644 --- a/doc/htmldoc/conf.py +++ b/doc/htmldoc/conf.py @@ -314,4 +314,3 @@ def copy_acknowledgments_file(src): copy_example_file(source_dir / "pynest/examples/Potjans_2014/microcircuit.png") copy_example_file(source_dir / "pynest/examples/Potjans_2014/README.rst") copy_example_file(source_dir / "pynest/examples/hpc_benchmark_connectivity.svg") -