From 11392cf43c6aa236f05f393442b29c76ac3411ff Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sat, 27 Apr 2024 07:57:48 +0100 Subject: [PATCH 1/9] Fix CI --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index c681d548d..862ab2b82 100644 --- a/environment.yml +++ b/environment.yml @@ -43,7 +43,7 @@ dependencies: - moviepy # used for notebook testing - pytest - - python=3.9 + - python=3.10 - pip - pip: # extensions From a1d4035de4d2ae0e7e332612e19dbc97ab9fe4c0 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sat, 27 Apr 2024 08:59:40 +0100 Subject: [PATCH 2/9] unpin dask --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 862ab2b82..4a6b196e0 100644 --- a/environment.yml +++ b/environment.yml @@ -36,8 +36,8 @@ dependencies: - scikit-image - seaborn>=0.12.1 # parallelization - - distributed==2021.1.0 - - dask==2021.1.0 + - distributed + - dask # used for visualising/making movies of molecules; - nglview - moviepy From 2eb7043d8a9d71e08907e879c15468efed636659 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sat, 27 Apr 2024 09:08:45 +0100 Subject: [PATCH 3/9] remove explicit python version --- .github/workflows/pre-commit.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml index b9d74b0e0..d288496ac 100644 --- a/.github/workflows/pre-commit.yaml +++ b/.github/workflows/pre-commit.yaml @@ -23,7 +23,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: setup micromamba uses: mamba-org/setup-micromamba@v1 @@ -31,7 +31,6 @@ jobs: environment-file: environment.yml environment-name: mda-user-guide create-args: >- - python=3.9 pip condarc: | channels: From 648fdd7f9ad90a7d4c133cf0c09014eade03b902 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sat, 27 Apr 2024 09:10:42 +0100 Subject: [PATCH 4/9] temp branch switch --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 4a6b196e0..3730bd655 100644 --- a/environment.yml +++ b/environment.yml @@ -55,7 +55,7 @@ dependencies: # doc generation dependency - pygithub # mdanalysis and its tests and test data - - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=mdanalysis&subdirectory=package - - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=MDAnalysisTests&subdirectory=testsuite + - git+https://github.com/MDAnalysis/mdanalysis@fix-discovery#egg=mdanalysis&subdirectory=package + - git+https://github.com/MDAnalysis/mdanalysis@fix-discovery#egg=MDAnalysisTests&subdirectory=testsuite - git+https://github.com/MDAnalysis/MDAnalysisData@master#egg=MDAnalysisData - syrupy # snapshot tests From 580031a6384051dbc3552ba68c0652d9760d5fd8 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sat, 27 Apr 2024 09:32:30 +0100 Subject: [PATCH 5/9] fix hole2 notebook --- doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb b/doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb index 9be537a71..3f78e0dda 100644 --- a/doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb +++ b/doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb @@ -293,7 +293,7 @@ "outputs": [ { "data": { - "text/plain": "" + "text/plain": "" }, "execution_count": 7, "metadata": {}, From e64bf1c621c3bbde75286a2f32601c00c4a8e441 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sat, 27 Apr 2024 09:47:52 +0100 Subject: [PATCH 6/9] skip problematic cells --- .../analysis/reduced_dimensions/diffusion_map.ipynb | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb b/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb index 91eaac630..f1f2eb91b 100644 --- a/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb +++ b/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb @@ -145,7 +145,11 @@ "text/plain": "array([0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525])" }, "execution_count": 4, - "metadata": {}, + "metadata": { + "tags": [ + "nbval-ignore-output" + ] + }, "output_type": "execute_result" } ], @@ -248,7 +252,11 @@ "text/html": "
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Mode2Mode3Mode4Mode5Mode6Time (ps)
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" }, "execution_count": 7, - "metadata": {}, + "metadata": { + "tags": [ + "nbval-ignore-output" + ] + }, "output_type": "execute_result" } ], From 092d857abdd2f462701ee65f886686fe9a7ed53f Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sat, 27 Apr 2024 10:07:38 +0100 Subject: [PATCH 7/9] move tags around a bit --- .../reduced_dimensions/diffusion_map.ipynb | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb b/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb index f1f2eb91b..32aebc778 100644 --- a/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb +++ b/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb @@ -137,7 +137,8 @@ "ExecuteTime": { "end_time": "2023-12-01T15:45:48.442257804Z", "start_time": "2023-12-01T15:45:48.414223207Z" - } + }, + "tags": ["nbval-ignore-output"], }, "outputs": [ { @@ -145,11 +146,7 @@ "text/plain": "array([0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525, 0.10101525, 0.10101525,\n 0.10101525, 0.10101525, 0.10101525])" }, "execution_count": 4, - "metadata": { - "tags": [ - "nbval-ignore-output" - ] - }, + "metadata": {}, "output_type": "execute_result" } ], @@ -243,7 +240,8 @@ "ExecuteTime": { "end_time": "2023-12-01T15:46:16.586512021Z", "start_time": "2023-12-01T15:46:16.569047940Z" - } + }, + "tags": ["nbval-ignore-output"] }, "outputs": [ { @@ -252,11 +250,7 @@ "text/html": "
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Mode2Mode3Mode4Mode5Mode6Time (ps)
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40.2503840.1718730.1034070.0571430.0283984.0
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" }, "execution_count": 7, - "metadata": { - "tags": [ - "nbval-ignore-output" - ] - }, + "metadata": {}, "output_type": "execute_result" } ], From 1c4fc876c9c39832c17f728416437b76c778e486 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sat, 27 Apr 2024 10:16:02 +0100 Subject: [PATCH 8/9] fix additional comma --- .../examples/analysis/reduced_dimensions/diffusion_map.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb b/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb index 32aebc778..1022a38c5 100644 --- a/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb +++ b/doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb @@ -138,7 +138,7 @@ "end_time": "2023-12-01T15:45:48.442257804Z", "start_time": "2023-12-01T15:45:48.414223207Z" }, - "tags": ["nbval-ignore-output"], + "tags": ["nbval-ignore-output"] }, "outputs": [ { From 1bcb073c496db06a3a51f0d51064ae24004983e0 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 28 Apr 2024 21:26:26 +0100 Subject: [PATCH 9/9] Update environment.yml --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 3730bd655..4a6b196e0 100644 --- a/environment.yml +++ b/environment.yml @@ -55,7 +55,7 @@ dependencies: # doc generation dependency - pygithub # mdanalysis and its tests and test data - - git+https://github.com/MDAnalysis/mdanalysis@fix-discovery#egg=mdanalysis&subdirectory=package - - git+https://github.com/MDAnalysis/mdanalysis@fix-discovery#egg=MDAnalysisTests&subdirectory=testsuite + - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=mdanalysis&subdirectory=package + - git+https://github.com/MDAnalysis/mdanalysis@develop#egg=MDAnalysisTests&subdirectory=testsuite - git+https://github.com/MDAnalysis/MDAnalysisData@master#egg=MDAnalysisData - syrupy # snapshot tests