From 4323ba8ee88d5c593f201b7264bb3742704d7658 Mon Sep 17 00:00:00 2001 From: Jan Domanski Date: Tue, 8 Aug 2023 13:29:59 +0100 Subject: [PATCH 01/11] dev: comment and cleanup environment.yml --- environment.yml | 75 +++++++++++++++++++++++++++---------------------- 1 file changed, 42 insertions(+), 33 deletions(-) diff --git a/environment.yml b/environment.yml index 0807ae729..95879f6a6 100644 --- a/environment.yml +++ b/environment.yml @@ -5,57 +5,66 @@ channels: - plotly - defaults dependencies: + # mdanalysis dependencies - cython - - distributed==2021.1.0 - - dask==2021.1.0 - - python-graphviz - - pytest - - decorator - - docutils - - graphviz - - ipywidgets<8.0.0 - - ipython - - ipygany - - jedi - - jinja2 - - jupyter_contrib_nbextensions - matplotlib - - nbclient - - nbconvert - - nbformat - - nbsphinx - networkx - - nglview - - notebook - numpy + - openmm>=7.0.0 - packaging - parmed - - parso - - pip - - plotly - - pybtex - - python=3.9 - - pyvista - - scikit-image - scikit-learn>=1.1.2 + - threadpoolctl + # building documentation + - docutils + - pandoc + - pybtex - sphinx - sphinxcontrib-bibtex - - threadpoolctl + # used by custom_parallel_analysis.ipynb + - graphviz - tabulate - - widgetsnbextension - - ipycytoscape>=1.3.0 + - python-graphviz + # used in multiple notebooks + - jupyter_contrib_nbextensions + - nbconvert + - nbformat + - nglview + - notebook<7 - seaborn>=0.12.1 - - openmm>=7.0.0 - - pandoc + # used in pairwise_rmsd.ipynb + - plotly + # used in custom_parallel_analysis.ipynb + - distributed==2021.1.0 + - dask==2021.1.0 + # used in density_analysis.ipynb + - ipygany + # used in density_analysis.ipynb + - pyvista + # used in density_analysis.ipynb + - scikit-image + # used in aligning_trajectory.ipynb - moviepy - - ipyvtklink + # used in conf.py + - ipython + - ipywidgets<8.0.0 + - nbsphinx + # used for notebook testing + - pytest + - python=3.9 + - pip - pip: - - sphinx_rtd_theme + # used in conf.py - msmb_theme + - sphinx_rtd_theme - sphinx-sitemap + # used for notebook testing - nbval + # developer tooling - pre-commit + # mdanalysis dependencies - pyedr>=0.7 + # 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/MDAnalysisData@master#egg=MDAnalysisData From a18752e84b6be94aaaf763cfe067dea9b101f046 Mon Sep 17 00:00:00 2001 From: Jan Domanski Date: Fri, 18 Aug 2023 13:29:28 +0200 Subject: [PATCH 02/11] review: comments by Irfan --- environment.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 95879f6a6..d8a6ab5e9 100644 --- a/environment.yml +++ b/environment.yml @@ -6,15 +6,14 @@ channels: - defaults dependencies: # mdanalysis dependencies - - cython - matplotlib - networkx - - numpy - openmm>=7.0.0 - packaging - parmed - scikit-learn>=1.1.2 - threadpoolctl + - pyedr>=0.7 # building documentation - docutils - pandoc @@ -62,8 +61,6 @@ dependencies: - nbval # developer tooling - pre-commit - # mdanalysis dependencies - - pyedr>=0.7 # 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 From db5399e1143c421038a1cf0ac204ac4400e45054 Mon Sep 17 00:00:00 2001 From: Jan Domanski Date: Fri, 18 Aug 2023 13:35:01 +0200 Subject: [PATCH 03/11] review: comments from Lily --- environment.yml | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/environment.yml b/environment.yml index d8a6ab5e9..20f73239c 100644 --- a/environment.yml +++ b/environment.yml @@ -24,25 +24,22 @@ dependencies: - graphviz - tabulate - python-graphviz - # used in multiple notebooks + # extensions - jupyter_contrib_nbextensions - - nbconvert + - nbconvert # not called by any notebook explicitly but to download notebooks, or in nbsphinx - nbformat - - nglview - notebook<7 - - seaborn>=0.12.1 - # used in pairwise_rmsd.ipynb + # used for visualising/plotting - plotly - # used in custom_parallel_analysis.ipynb - - distributed==2021.1.0 - - dask==2021.1.0 - # used in density_analysis.ipynb - ipygany - # used in density_analysis.ipynb - pyvista - # used in density_analysis.ipynb - scikit-image - # used in aligning_trajectory.ipynb + - seaborn>=0.12.1 + # parallelization + - distributed==2021.1.0 + - dask==2021.1.0 + # used for visualising/making movies of molecules; + - nglview - moviepy # used in conf.py - ipython From bc99e7b0dde7237f1de205a67614ceec4bd91042 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Doma=C5=84ski?= Date: Sun, 20 Aug 2023 13:40:12 +0100 Subject: [PATCH 04/11] Update environment.yml Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 20f73239c..4d5323d59 100644 --- a/environment.yml +++ b/environment.yml @@ -50,7 +50,7 @@ dependencies: - python=3.9 - pip - pip: - # used in conf.py + # docs themes - msmb_theme - sphinx_rtd_theme - sphinx-sitemap From 09c2ba8a6c41cf6c63b4418c39c553a7e6cc3ccb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Doma=C5=84ski?= Date: Sun, 20 Aug 2023 13:40:17 +0100 Subject: [PATCH 05/11] Update environment.yml Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index 4d5323d59..cfff0318d 100644 --- a/environment.yml +++ b/environment.yml @@ -53,6 +53,7 @@ dependencies: # docs themes - msmb_theme - sphinx_rtd_theme + # extensions - sphinx-sitemap # used for notebook testing - nbval From 0bf3c8e0049b1f14257d960f1c3ee605e7bd0ff7 Mon Sep 17 00:00:00 2001 From: Jan Domanski Date: Sun, 20 Aug 2023 14:41:59 +0200 Subject: [PATCH 06/11] review: comments from Lily --- environment.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index cfff0318d..31dea4fe7 100644 --- a/environment.yml +++ b/environment.yml @@ -20,18 +20,17 @@ dependencies: - pybtex - sphinx - sphinxcontrib-bibtex - # used by custom_parallel_analysis.ipynb - - graphviz - tabulate - - python-graphviz # extensions - jupyter_contrib_nbextensions - nbconvert # not called by any notebook explicitly but to download notebooks, or in nbsphinx - nbformat - notebook<7 # used for visualising/plotting - - plotly + - graphviz - ipygany + - plotly + - python-graphviz - pyvista - scikit-image - seaborn>=0.12.1 From 2c876be7682abea46c26208be1815c2f347d6190 Mon Sep 17 00:00:00 2001 From: Jan Domanski Date: Mon, 21 Aug 2023 12:19:49 +0200 Subject: [PATCH 07/11] update environment.yml --- environment.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 31dea4fe7..80c461e84 100644 --- a/environment.yml +++ b/environment.yml @@ -22,9 +22,12 @@ dependencies: - sphinxcontrib-bibtex - tabulate # extensions + - ipython + - ipywidgets<8.0.0 - jupyter_contrib_nbextensions - nbconvert # not called by any notebook explicitly but to download notebooks, or in nbsphinx - nbformat + - nbsphinx - notebook<7 # used for visualising/plotting - graphviz @@ -40,10 +43,6 @@ dependencies: # used for visualising/making movies of molecules; - nglview - moviepy - # used in conf.py - - ipython - - ipywidgets<8.0.0 - - nbsphinx # used for notebook testing - pytest - python=3.9 From fae4e8257a99f217fbe3abf93c2e44ab4fcb2797 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Doma=C5=84ski?= Date: Mon, 21 Aug 2023 20:52:32 +0100 Subject: [PATCH 08/11] Update environment.yml Co-authored-by: Irfan Alibay --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 80c461e84..b74bcebb2 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,6 @@ channels: - defaults dependencies: # mdanalysis dependencies - - matplotlib - networkx - openmm>=7.0.0 - packaging From b2d7e368577ee384cdf2858e8fcc92407c798c4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Doma=C5=84ski?= Date: Mon, 21 Aug 2023 20:52:43 +0100 Subject: [PATCH 09/11] Update environment.yml Co-authored-by: Irfan Alibay --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index b74bcebb2..6d61a32de 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,6 @@ channels: - defaults dependencies: # mdanalysis dependencies - - networkx - openmm>=7.0.0 - packaging - parmed From 2611b87eb7f7f72db3b6b9e84f60ec1fbcb52d4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Doma=C5=84ski?= Date: Mon, 21 Aug 2023 20:52:51 +0100 Subject: [PATCH 10/11] Update environment.yml Co-authored-by: Irfan Alibay --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 6d61a32de..9833b997b 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,6 @@ channels: dependencies: # mdanalysis dependencies - openmm>=7.0.0 - - packaging - parmed - scikit-learn>=1.1.2 - threadpoolctl From dd9aca2371587abdd35d1256056545e12edeb540 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Doma=C5=84ski?= Date: Mon, 21 Aug 2023 20:52:58 +0100 Subject: [PATCH 11/11] Update environment.yml Co-authored-by: Irfan Alibay --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 9833b997b..927d92ebc 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,6 @@ dependencies: - openmm>=7.0.0 - parmed - scikit-learn>=1.1.2 - - threadpoolctl - pyedr>=0.7 # building documentation - docutils