From 6376b2445a449bb4235ee34234d788ad186817c7 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Mon, 1 Apr 2024 16:40:27 -0300 Subject: [PATCH 1/9] Update files and change README to markdown --- LICENSE.txt => LICENSE | 0 MANIFEST.in | 4 ++-- README.md | 53 ++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 24 +++++++++---------- 4 files changed, 67 insertions(+), 14 deletions(-) rename LICENSE.txt => LICENSE (100%) create mode 100644 README.md diff --git a/LICENSE.txt b/LICENSE similarity index 100% rename from LICENSE.txt rename to LICENSE diff --git a/MANIFEST.in b/MANIFEST.in index c24b4da7..a7c7d17c 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -10,10 +10,10 @@ include pyKVFinder/data/tests/*.pdb include pyKVFinder/data/tests/*.xyz # Include the license file -include LICENSE.txt +include LICENSE # Include README -include README.rst +include README.md # Include Python requirements include requirements.txt diff --git a/README.md b/README.md new file mode 100644 index 00000000..e32ac5f6 --- /dev/null +++ b/README.md @@ -0,0 +1,53 @@ +# pyKVFinder + +![PyPI](https://img.shields.io/pypi/v/pyKVFinder) +![Python](https://img.shields.io/pypi/pyversions/pyKVFinder) +![PyPI Downloads](https://img.shields.io/pypi/dm/pyKVFinder) +![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing) +![Integration testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing) +![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build) +![Coverage](https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg) + +A Python package for detecting and characterizing biomolecular cavities. + +See also: + +- [GitHub repository](https://github.com/LBC-LNBio/pyKVFinder/) +- [Documentation and tutorial](https://lbc-lnbio.github.io/pyKVFinder/) + +## Installation + +To install the latest release on +[PyPI](https://pypi.org/project/pyKVFinder), run: + + pip install pyKVFinder + +Or to install the latest developmental version, run: + + git clone https://github.com/LBC-LNBio/pyKVFinder.git + pip install pyKVFinder + +## Citation + +If you use *pyKVFinder* package, please cite: + +Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O., +Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an +efficient and integrable Python package for biomolecular cavity +detection and characterization in data science. BMC bioinformatics, +22(1), 607. . + +If you use *pyKVFinder.Molecule*, please also cite: + +Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P. +S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular +Cages. Journal of chemical information and modeling, 63(12), 3772-3785. +. + +## License + +The software is licensed under the terms of the GNU General Public +License version 3 (GPL3) and is distributed in the hope that it will be +useful, but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +Public License for more details. diff --git a/pyproject.toml b/pyproject.toml index 62a6ee31..3ec78a07 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,19 +11,18 @@ build-backend = "setuptools.build_meta" name = "pyKVFinder" description = "Python package to detect and characterize cavities in biomolecular structures" authors = [ - { name = "João Victor da Silva Guerra", email = "jvsguerra@gmail.com" }, - { name = "Helder Veras Ribeiro Filho" }, - { name = "Luiz Fernando Giolo Alves" }, - { name = "Gabriel Ernesto Jara" }, - { name = "Leandro Oliveira Bortot" }, - { name = "José Geraldo de Carvalho Pereira" }, - { name = "Paulo Sergio Lopes-de-Oliveira" }, + { name = "João V. S. Guerra", email = "jvsguerra@gmail.com" }, + { name = "Helder V. Ribeiro-Filho" }, + { name = "Luiz F. G. Alves" }, + { name = "Pablo W. A. Silva" }, + { name = "Gabriel E. Jara" }, + { name = "Leandro O. Bortot" }, + { name = "José G. C. Pereira" }, + { name = "Paulo S. Lopes-de-Oliveira" }, ] -maintainers = [ - { name = "João Victor da Silva Guerra", email = "jvsguerra@gmail.com" }, -] -license = { file = "LICENSE.txt" } -readme = { file = "README.rst", content-type = "text/x-rst" } +maintainers = [{ name = "João V. S. Guerra", email = "jvsguerra@gmail.com" }] +license = { file = "LICENSE" } +readme = { file = "README.md", content-type = "text/markdown" } requires-python = ">=3.9" keywords = [ "structural biology", @@ -31,6 +30,7 @@ keywords = [ "biomolecules", "cavity detection", "cavity characterization", + "binding sites", ] classifiers = [ "Development Status :: 4 - Beta", From 37abfd8f47084b9ebaf605ceeeaf866aab99acd0 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Mon, 1 Apr 2024 16:55:37 -0300 Subject: [PATCH 2/9] Update README.md --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index e32ac5f6..6d166cc4 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ # pyKVFinder -![PyPI](https://img.shields.io/pypi/v/pyKVFinder) -![Python](https://img.shields.io/pypi/pyversions/pyKVFinder) -![PyPI Downloads](https://img.shields.io/pypi/dm/pyKVFinder) -![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing) -![Integration testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing) -![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build) +![PyPI - Version](https://img.shields.io/pypi/v/pyKVFinder?link=https%3A%2F%2Fpypi.org%2Fproject%2FpyKVFinder%2F) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyKVFinder?link=https%3A%2F%2Fpypi.org%2Fproject%2FpyKVFinder%2F) +![PyPI - Downloads](https://img.shields.io/pypi/dm/pyKVFinder) +![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%unit-testing.yml) +![Integration testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%integration-testing.yml) +![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%2Fdeploy.yml) ![Coverage](https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg) A Python package for detecting and characterizing biomolecular cavities. From e16c9b2329c836857d4ed7dcba97965b31d0e18f Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Mon, 1 Apr 2024 16:57:21 -0300 Subject: [PATCH 3/9] Update README.md --- README.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6d166cc4..16a91bcf 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # pyKVFinder -![PyPI - Version](https://img.shields.io/pypi/v/pyKVFinder?link=https%3A%2F%2Fpypi.org%2Fproject%2FpyKVFinder%2F) +[![PyPI - Version](https://img.shields.io/pypi/v/pyKVFinder)](https://pypi.org/project/pyKVFinder/) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyKVFinder?link=https%3A%2F%2Fpypi.org%2Fproject%2FpyKVFinder%2F) ![PyPI - Downloads](https://img.shields.io/pypi/dm/pyKVFinder) ![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%unit-testing.yml) @@ -8,6 +8,21 @@ ![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%2Fdeploy.yml) ![Coverage](https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg) + + + + + + + + + A Python package for detecting and characterizing biomolecular cavities. See also: From f23a1069bd21eb8e9319478901623b1308843e98 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Mon, 1 Apr 2024 17:01:33 -0300 Subject: [PATCH 4/9] Update README.md --- README.md | 27 ++++++--------------------- 1 file changed, 6 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 16a91bcf..b9ca6ed2 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,12 @@ # pyKVFinder [![PyPI - Version](https://img.shields.io/pypi/v/pyKVFinder)](https://pypi.org/project/pyKVFinder/) -![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyKVFinder?link=https%3A%2F%2Fpypi.org%2Fproject%2FpyKVFinder%2F) -![PyPI - Downloads](https://img.shields.io/pypi/dm/pyKVFinder) -![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%unit-testing.yml) -![Integration testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%integration-testing.yml) -![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build&link=https%3A%2F%2Fgithub.com%2FLBC-LNBio%2FpyKVFinder%2Factions%2Fworkflows%2Fdeploy.yml) -![Coverage](https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg) - - - - - - - - - +[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyKVFinder)](https://pypi.org/project/pyKVFinder/) +[![PyPI - Downloads](https://img.shields.io/pypi/dm/pyKVFinder)](https://pypi.org/project/pyKVFinder/) +[![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing)](https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/unit-testing.yml) +[![Integration testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing)](https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/integration-testing.yml) +[![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build)](https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/deploy.yml) +[![Coverage](https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg)](https://github.com/LBC-LNBio/pyKVFinder/blob/coverage/coverage.txt) A Python package for detecting and characterizing biomolecular cavities. From a896422afcabe8c2263b4cec070fe33fee843750 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Mon, 1 Apr 2024 17:01:49 -0300 Subject: [PATCH 5/9] Update README.md --- README.rst | 68 ------------------------------------------------------ 1 file changed, 68 deletions(-) delete mode 100644 README.rst diff --git a/README.rst b/README.rst deleted file mode 100644 index cd798528..00000000 --- a/README.rst +++ /dev/null @@ -1,68 +0,0 @@ -########## -pyKVFinder -########## - -.. image:: https://img.shields.io/pypi/v/pyKVFinder - :target: https://pypi.org/project/pyKVFinder/ - -.. image:: https://img.shields.io/pypi/pyversions/pyKVFinder - :target: https://pypi.org/project/pyKVFinder/ - -.. image:: https://img.shields.io/pypi/dm/pyKVFinder - :target: https://pypi.org/project/pyKVFinder/ - -.. image:: https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing - :target: https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/unit-testing.yml - -.. image:: https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing - :target: https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/integration-testing.yml - -.. image:: https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build - :target: https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/deploy.yml - -.. image:: https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg - - -A Python package for detecting and characterizing biomolecular cavities. - -See also: - -* `GitHub repository `_ -* `Documentation and tutorial `_ - -************ -Installation -************ - -To install the latest release on `PyPI `_, -run: - -:: - - pip install pyKVFinder - -Or to install the latest developmental version, run: - -:: - - git clone https://github.com/LBC-LNBio/pyKVFinder.git - pip install pyKVFinder - -******** -Citation -******** - -If you use pyKVFinder package, please cite: - -Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O., Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC bioinformatics, 22(1), 607. https://doi.org/10.1186/s12859-021-04519-4. - -If you use *pyKVFinder.Molecule*, please also cite: - -Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P. S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular Cages. Journal of chemical information and modeling, 63(12), 3772-3785. https://doi.org/10.1021/acs.jcim.3c00328. - - -******* -License -******* - -The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. From 671ef0b1021241f655190b8535e43c9d8fb601eb Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Wed, 24 Apr 2024 17:43:05 -0300 Subject: [PATCH 6/9] Add pylint to workflows --- .github/workflows/pylint.yml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 .github/workflows/pylint.yml diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml new file mode 100644 index 00000000..beffe2be --- /dev/null +++ b/.github/workflows/pylint.yml @@ -0,0 +1,27 @@ +name: Pylint + +on: [push] + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12"] + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install pylint + + - name: Analysing the code with pylint + run: | + pylint $(git ls-files 'pyKVFinder/*.py') From 9a96e2d4087bcd5733f46f73758186f8b3712d7c Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Wed, 24 Apr 2024 17:58:49 -0300 Subject: [PATCH 7/9] Update pylint to workflows --- .github/workflows/pylint.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml index beffe2be..103dd802 100644 --- a/.github/workflows/pylint.yml +++ b/.github/workflows/pylint.yml @@ -24,4 +24,10 @@ jobs: - name: Analysing the code with pylint run: | - pylint $(git ls-files 'pyKVFinder/*.py') + pylint $(git ls-files 'pyKVFinder/*.py') --output=pylint.txt || true + + - name: Upload pylint report + uses: actions/upload-artifact@v3 + with: + name: artifacts + path: ./pylint.txt From 5a13ea07e5c263366db1c5a4e70abcf0d75fa5a6 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Wed, 24 Apr 2024 18:05:34 -0300 Subject: [PATCH 8/9] Update coverage workflow --- .github/workflows/coverage.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 83cc0621..4c84db5a 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -36,10 +36,10 @@ jobs: default-branch: master remove-link-from-badge: true - - name: Coverage Bagdge - uses: tj-actions/coverage-badge-py@v2 - with: - output: coverage/coverage.svg + # - name: Coverage Bagdge + # uses: tj-actions/coverage-badge-py@v2 + # with: + # output: coverage/coverage.svg - name: Publish coverage report to coverage branch uses: JamesIves/github-pages-deploy-action@v4 From dda55bb793cbd8b3a060c13fd37e9cab8ed48df8 Mon Sep 17 00:00:00 2001 From: jvsguerra Date: Thu, 25 Apr 2024 16:01:04 -0300 Subject: [PATCH 9/9] Update coverage workflow --- .github/workflows/coverage.yml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 4c84db5a..560f9b2f 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -26,20 +26,24 @@ jobs: - name: Build coverage file run: | - mkdir coverage - pytest --cov=pyKVFinder --cov-report=term-missing | tee coverage/coverage.txt + pytest --cov=pyKVFinder --cov-report=term-missing | tee coverage.txt - name: Pytest coverage comment uses: MishaKav/pytest-coverage-comment@main with: - pytest-coverage-path: coverage/coverage.txt + pytest-coverage-path: coverage.txt default-branch: master remove-link-from-badge: true - # - name: Coverage Bagdge - # uses: tj-actions/coverage-badge-py@v2 - # with: - # output: coverage/coverage.svg + - name: Coverage Bagdge + uses: tj-actions/coverage-badge-py@v2 + with: + output: coverage.svg + + - name: Move report to coverage directory + run: | + mkdir coverage + mv coverage.txt coverage.svg coverage/ - name: Publish coverage report to coverage branch uses: JamesIves/github-pages-deploy-action@v4