From e402a16763cec6324dee48524e6d4985ec0045be Mon Sep 17 00:00:00 2001 From: Alia Lescoulie <72271618+ALescoulie@users.noreply.github.com> Date: Mon, 17 Apr 2023 13:14:28 -0700 Subject: [PATCH 1/9] Create metadata.yaml --- mdakits/mdsapt/metadata.yaml | 59 ++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 mdakits/mdsapt/metadata.yaml diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml new file mode 100644 index 00000000..65b23fbc --- /dev/null +++ b/mdakits/mdsapt/metadata.yaml @@ -0,0 +1,59 @@ +# Required entries +## str: name of the project (the respository name) +project_name: MD-SAPT +## List(str): a list of authors (or a link to the authors file) +authors: + - Alia Lescoulie + - Astrid Yu + - Ashley Ringer McDonald +## List(str): a list of maintainers +maintainers: + - Alia Lescoulie + - Ashley Ringer McDonald +## str: a free form description of the mdakit +description: + SAPT calculations on MD data using Psi4 +## List(str): a list of keywords which describe the mdakit +keywords: + - SAPT + - protein + - quantum +## str: the license the mdakit falls under +license: GPL-2.0-or-later +## str: the link to the project's code +project_home: https://github.com/calpolyccg/MDSAPT +## str: the link to the project's documentation +documentation_home: https://mdsapt.readthedocs.io +## str: the type of documentation available [UserGuide, API, README] +documentation_type: UserGuide + API + +# Optional entries +## List(str): a list of commands to use when installing the latest +## release of the code. Note: only one installation method can currently +## be defined. We suggest using conda/mamba where possible. +install: + - conda install -c psi4 mdsapt +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/calpolyccg/MDSAPT@master +## str: the package name used to import the mdakit +import_name: mdsapt +## str: a specification for the range of Python versions supported by this MDAKit +python_requires: ">=3.8" +## str: a specification for the range of MDAnalysis versions supported by this MDAKit +mdanalysis_requires: ">=2.0.0" +## List(str): a list of commands to use when attempting to run the MDAKit's tests +run_tests: + - pytest --pyargs propkatraj.tests +## List(str): a list of commands to use to install the necessary dependencies required +## to run the MDAKit's tests +test_dependencies: +project_org: Becksteinlab +## str: the development status of the MDAKit +development_status: Mature +## List(str) a list of publications to cite when using the MDAKit +publications: +community_home: +## str: a link to the MDAKit's changelog +changelog: From ac07c2198abcb3c8fba2cb8d1d6a9eb107159284 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 18 Sep 2023 10:56:10 -0400 Subject: [PATCH 2/9] Update metadata.yaml --- mdakits/mdsapt/metadata.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index 65b23fbc..51fa867f 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -19,7 +19,7 @@ keywords: - protein - quantum ## str: the license the mdakit falls under -license: GPL-2.0-or-later +license: GPL-3.0-or-later ## str: the link to the project's code project_home: https://github.com/calpolyccg/MDSAPT ## str: the link to the project's documentation @@ -32,7 +32,7 @@ documentation_type: UserGuide + API ## release of the code. Note: only one installation method can currently ## be defined. We suggest using conda/mamba where possible. install: - - conda install -c psi4 mdsapt + - mamba install -c psi4 mdsapt ## List(str): a list of commands to use when installing the mdakit from its ## source code. src_install: @@ -45,15 +45,15 @@ python_requires: ">=3.8" mdanalysis_requires: ">=2.0.0" ## List(str): a list of commands to use when attempting to run the MDAKit's tests run_tests: - - pytest --pyargs propkatraj.tests + - pytest --pyargs mdsapt.tests ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests test_dependencies: -project_org: Becksteinlab +project_org: calpolyccg ## str: the development status of the MDAKit development_status: Mature ## List(str) a list of publications to cite when using the MDAKit publications: community_home: ## str: a link to the MDAKit's changelog -changelog: +changelog: https://github.com/calpolyccg/MDSAPT/releases From 4f2f9edb7f79d37fb0ff5b211ab904057b964054 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 18 Sep 2023 11:22:40 -0400 Subject: [PATCH 3/9] install mdsapt properly - conda package requires dev label - install pre-requisites for source installation --- mdakits/mdsapt/metadata.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index 51fa867f..04c0bfa6 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -32,10 +32,12 @@ documentation_type: UserGuide + API ## release of the code. Note: only one installation method can currently ## be defined. We suggest using conda/mamba where possible. install: - - mamba install -c psi4 mdsapt + - mamba install -c psi4/label/dev -c conda-forge mdsapt ## List(str): a list of commands to use when installing the mdakit from its ## source code. src_install: + # required dependencies from environment.yaml + - mamba install -c psi4 -c conda-forge -c defaults "psi4>=1.6.1,<1.7" click numpy openmm pandas pdbfixer pytest pydantic pytest-cov pyyaml rdkit - pip install git+https://github.com/calpolyccg/MDSAPT@master ## str: the package name used to import the mdakit import_name: mdsapt From 1a676677e4f0e92ebf5c96d49726dc8606aecfb8 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Mon, 18 Sep 2023 11:38:43 -0400 Subject: [PATCH 4/9] get tests from checked out source --- mdakits/mdsapt/metadata.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index 04c0bfa6..fdb49ab9 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -47,7 +47,8 @@ python_requires: ">=3.8" mdanalysis_requires: ">=2.0.0" ## List(str): a list of commands to use when attempting to run the MDAKit's tests run_tests: - - pytest --pyargs mdsapt.tests + - git clone latest + - pytest -v ./mdsapt/tests ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests test_dependencies: From f6f007f6f09142cda77f058d617cf5c41dfa2bff Mon Sep 17 00:00:00 2001 From: Alia Lescoulie Date: Sun, 23 Jun 2024 20:46:54 -0700 Subject: [PATCH 5/9] add conda-forge install --- mdakits/mdsapt/metadata.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index fdb49ab9..7d23b8e2 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -9,6 +9,7 @@ authors: ## List(str): a list of maintainers maintainers: - Alia Lescoulie + - Astrid Yu - Ashley Ringer McDonald ## str: a free form description of the mdakit description: @@ -32,13 +33,13 @@ documentation_type: UserGuide + API ## release of the code. Note: only one installation method can currently ## be defined. We suggest using conda/mamba where possible. install: - - mamba install -c psi4/label/dev -c conda-forge mdsapt + - mamba install -c conda-forge mdsapt ## List(str): a list of commands to use when installing the mdakit from its ## source code. src_install: # required dependencies from environment.yaml - - mamba install -c psi4 -c conda-forge -c defaults "psi4>=1.6.1,<1.7" click numpy openmm pandas pdbfixer pytest pydantic pytest-cov pyyaml rdkit - - pip install git+https://github.com/calpolyccg/MDSAPT@master + mamba install -c conda-forge psi4 >= 1.9.1, mdanalysis >=2.7.0, rdkit >=2023.09.5, openmm >=8.1.1, pdbfixer >=1.9, numpy, click, pandas, pyarrow, pyyaml + pip install git+https://github.com/calpolyccg/MDSAPT@master ## str: the package name used to import the mdakit import_name: mdsapt ## str: a specification for the range of Python versions supported by this MDAKit @@ -51,8 +52,8 @@ run_tests: - pytest -v ./mdsapt/tests ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests -test_dependencies: -project_org: calpolyccg +test_dependencies: pytest pytest-cov +project_org: Cal Poly Computational Chemistry Group ## str: the development status of the MDAKit development_status: Mature ## List(str) a list of publications to cite when using the MDAKit From d30ea9d4a27050cb25289a8de8defac43ff4d785 Mon Sep 17 00:00:00 2001 From: Alia Lescoulie <72271618+ALescoulie@users.noreply.github.com> Date: Mon, 24 Jun 2024 12:35:48 -0700 Subject: [PATCH 6/9] make src-install into a list Co-authored-by: Irfan Alibay --- mdakits/mdsapt/metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index 7d23b8e2..d261f337 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -38,8 +38,8 @@ install: ## source code. src_install: # required dependencies from environment.yaml - mamba install -c conda-forge psi4 >= 1.9.1, mdanalysis >=2.7.0, rdkit >=2023.09.5, openmm >=8.1.1, pdbfixer >=1.9, numpy, click, pandas, pyarrow, pyyaml - pip install git+https://github.com/calpolyccg/MDSAPT@master + - mamba install -c conda-forge psi4 >= 1.9.1, mdanalysis >=2.7.0, rdkit >=2023.09.5, openmm >=8.1.1, pdbfixer >=1.9, numpy, click, pandas, pyarrow, pyyaml + - pip install git+https://github.com/calpolyccg/MDSAPT@master ## str: the package name used to import the mdakit import_name: mdsapt ## str: a specification for the range of Python versions supported by this MDAKit From 2001829853700444002b1b9905c44afbd9673695 Mon Sep 17 00:00:00 2001 From: Alia Lescoulie Date: Mon, 24 Jun 2024 13:01:35 -0700 Subject: [PATCH 7/9] fix test dependencies --- mdakits/mdsapt/metadata.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index d261f337..4edbdbfc 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -52,7 +52,8 @@ run_tests: - pytest -v ./mdsapt/tests ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests -test_dependencies: pytest pytest-cov +test_dependencies: + - mamba install pytest, pytest-cov project_org: Cal Poly Computational Chemistry Group ## str: the development status of the MDAKit development_status: Mature From a01a628896ae46ddedb32fe2f3f678557cf85dfc Mon Sep 17 00:00:00 2001 From: Alia Lescoulie Date: Tue, 2 Jul 2024 11:29:03 -0700 Subject: [PATCH 8/9] fix comma typo in test deps install --- mdakits/mdsapt/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index 4edbdbfc..b850fd58 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -53,7 +53,7 @@ run_tests: ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests test_dependencies: - - mamba install pytest, pytest-cov + - mamba install pytest pytest-cov project_org: Cal Poly Computational Chemistry Group ## str: the development status of the MDAKit development_status: Mature From 840e2a59813de0e88cab6f49554f521a030dafd0 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 2 Jul 2024 13:21:35 -0700 Subject: [PATCH 9/9] Update mdakits/mdsapt/metadata.yaml Co-authored-by: Irfan Alibay --- mdakits/mdsapt/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/mdsapt/metadata.yaml b/mdakits/mdsapt/metadata.yaml index b850fd58..f98bf9c7 100644 --- a/mdakits/mdsapt/metadata.yaml +++ b/mdakits/mdsapt/metadata.yaml @@ -38,7 +38,7 @@ install: ## source code. src_install: # required dependencies from environment.yaml - - mamba install -c conda-forge psi4 >= 1.9.1, mdanalysis >=2.7.0, rdkit >=2023.09.5, openmm >=8.1.1, pdbfixer >=1.9, numpy, click, pandas, pyarrow, pyyaml + - mamba install -c conda-forge "psi4>= 1.9.1" "mdanalysis >=2.7.0" "rdkit >=2023.09.5" "openmm >=8.1.1" "pdbfixer >=1.9" numpy click pandas pyarrow pyyaml - pip install git+https://github.com/calpolyccg/MDSAPT@master ## str: the package name used to import the mdakit import_name: mdsapt