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[2023.05.1-base] CI fixes and other housekeeping #345

Merged
merged 119 commits into from
May 24, 2023
Merged

[2023.05.1-base] CI fixes and other housekeeping #345

merged 119 commits into from
May 24, 2023

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mbackenkoehler
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@mbackenkoehler mbackenkoehler commented Apr 30, 2023 •
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Description

CI fixes and other housekeeping of current master branch.

Todos

Status

  • Ready to go

dominiquesydow and others added 21 commits December 28, 2022 23:01
@dominiquesydow
Create new branch!
98b95a2
@dominiquesydow
Merge branch 'base-ci-env-fix' into t019-fix-ligand-template
6b401f3
@dominiquesydow
T019: Remove simtk from docstrings [skip ci]
aab586c
@dominiquesydow
Merge branch 'base-ci-env-fix' into t019-fix-ligand-template
0ec6ee4
@dominiquesydow
CI: Run only T019 (tmp)
6fa544b
@dominiquesydow
Merge branch 'base-ci-env-fix' into t019-fix-ligand-template
0e49e24
@greglandrum
update to using fingerprint generator
520e4fd
@mbackenkoehler
replace deprecated Series.append
c0fca45
@mbackenkoehler
try re-running T004 to reset output
589733d
@mbackenkoehler
re-run more talktorials (7,10,11,14,21,23,24,25,26,27)
58902da
@mbackenkoehler
re-run T022
c7a5f6f
@mbackenkoehler
re-run T018
e4e3591
@mbackenkoehler
switch to linkinator
e671922
@mbackenkoehler
no reason to exclude localhost:8000
8441fea
@mbackenkoehler
tweak linkinator args
0e6f191
@hamzaibrahim21
add new email address
36bb288
@hamzaibrahim21
fix dead links
7a72203
@hamzaibrahim21
Ignore mp4 files
ba8a4c8
@mbackenkoehler
Merge pull request #344 from volkamerlab/master
2eecfe9 
Update dev branch
@mbackenkoehler
Merge pull request #331 from volkamerlab/328-update-notebooks-to-pand…
08aeda9 
…as200

T002: Fix usage of deprecated pandas function
@mbackenkoehler
Merge pull request #332 from volkamerlab/329-ci-new-pandas-formatting
7efbbd7 
Fixing pytest nbval fails
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@mbackenkoehler mbackenkoehler added the work-in-progress Work still ongoing label Apr 30, 2023
mbackenkoehler and others added 27 commits May 22, 2023 10:04
@mbackenkoehler
T001: re-run
51385a6
@mbackenkoehler
Merge remote-tracking branch 'refs/remotes/origin/dev' into dev
fee0a9b
@mbackenkoehler
Revert "CI: try caching for mamba"
40584af 
This reverts commit 0370208.
@mbackenkoehler
T019: incorporate Davids fix in #308
c6bf5b5
@mbackenkoehler
CI: reactivate test for all notebooks
4ec048e
@mbackenkoehler
Merge pull request #308 from volkamerlab/t019-fix-ligand-template
b9ea2d9 
T019: Fix "No template found for residue 444 (03P)"
@mbackenkoehler
T019: black
afd1e43
@mbackenkoehler
CI: update checkout and setup-pyhon actions
dcd3ba1
@mbackenkoehler
T019: split cell to avoid warning in output check
f1e2442
@mbackenkoehler
CI: cleanup temp files
0a38766
@mbackenkoehler
T019: black
e2b2e44
@dominiquesydow
CI: Exclude T019 under Windows from CI
b97bd83
@dominiquesydow
CI: Add "dev" branch to PR CI
2f6a5e0
@dominiquesydow
T020: fix deprecation warnings
9515565
@dominiquesydow
T020: add xtc offset files (add lock, update npz)
e356267
@dominiquesydow
CI: add tmp branch to CI
c8b39d2
@dominiquesydow
T020: remove xtc offset files
f2878ee
@dominiquesydow
CI: tmp run only T020
eb45383
@dominiquesydow
CI: run full CI again
456b81a
@mbackenkoehler
Merge pull request #363 from volkamerlab/t020-update-deprecated-code-…
d925e25 
…fix-broken-ci

T020: update deprecated code fix broken ci
@mbackenkoehler
Merge pull request #362 from volkamerlab/t019-exclude-windows-from-ci
2cb64f9 
CI: Exclude T019 again from Windows CI
@mbackenkoehler
T018: re-run
6fc30ab
@mbackenkoehler
CI: ignore T020 under mac; minor refactoring
e3cedf0
@mbackenkoehler
CI: temporary change! activate CI for feature branch
55a1c58
@mbackenkoehler
CI: Test ignoring T019 under macOS
72f8a09
@mbackenkoehler
Merge pull request #365 from volkamerlab/364-t020-not-working-under-m…
a3cf33c 
…ac-os

364 t020 not working under mac os
@mbackenkoehler
CI: remove temporary hook
0bf84aa
@AndreaVolkamer AndreaVolkamer self-requested a review May 24, 2023 12:58
AndreaVolkamer
AndreaVolkamer approved these changes May 24, 2023
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Thanks all for your help to get this running!

@AndreaVolkamer AndreaVolkamer merged commit b2b75e1 into master May 24, 2023
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@AndreaVolkamer AndreaVolkamer AndreaVolkamer approved these changes

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6 participants
@mbackenkoehler @AndreaVolkamer @dominiquesydow @greglandrum @hamzaibrahim21 @AAriam