From 8eedb3fb3d5c182479451fea52dd568ec5daa6e4 Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 09:51:26 +0100 Subject: [PATCH 01/13] Move to gh-actions. --- .github/workflows/tests.yml | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 .github/workflows/tests.yml diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 00000000..3dffb9a9 --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,38 @@ +name: tests + +on: + push: + branches: + - develop + - master + pull_request: + branches: + - develop + - master + +jobs: + test: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.7", "3.8"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: 'pip' + - name: install + run: | + python -m pip install --upgrade pip poetry + poetry install --extras docs + - name: unit-tests + run: | + poetry run pytest -v --cov=mdbenchmark + -name: docs + run: | + cd docs + poetry run make build From c96da65c994a4ef76f2a374592232ae8aa78c517 Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 10:33:40 +0100 Subject: [PATCH 02/13] Fix workflow. --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 3dffb9a9..ed292b50 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -32,7 +32,7 @@ jobs: - name: unit-tests run: | poetry run pytest -v --cov=mdbenchmark - -name: docs + - name: docs run: | cd docs poetry run make build From ed8fdd8fd5e6062e515e0f6167e99f3f8a3d15ab Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 10:55:11 +0100 Subject: [PATCH 03/13] Fix cache for setup-python. --- .github/workflows/tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ed292b50..6f41567c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -20,11 +20,13 @@ jobs: steps: - uses: actions/checkout@v3 + - name: Install poetry + run: pip install poetry - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - cache: 'pip' + cache: 'poetry' - name: install run: | python -m pip install --upgrade pip poetry From 2bd1ad457ca4f6885b77681d7e446c10c2d02e4d Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 11:56:16 +0100 Subject: [PATCH 04/13] Add upload to codecov. --- .github/workflows/tests.yml | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6f41567c..99ca229c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -17,6 +17,8 @@ jobs: strategy: matrix: python-version: ["3.7", "3.8"] + env: + PYTHON: ${{ matrix.python-version }} steps: - uses: actions/checkout@v3 @@ -27,14 +29,19 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: 'poetry' - - name: install + - name: Install mdbenchmark run: | python -m pip install --upgrade pip poetry poetry install --extras docs - - name: unit-tests - run: | - poetry run pytest -v --cov=mdbenchmark - - name: docs + - name: Unit-tests + run: poetry run pytest -v --cov=mdbenchmark + - name: Upload coverage + uses: codecov/codecov-action@v3 + with: + env_vars: PYTHON + fail_ci_if_error: true + - name: Make docs run: | cd docs poetry run make build + From 1c73b2b4aa8a70669889e042088069525f61225d Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 13:34:22 +0100 Subject: [PATCH 05/13] Explicitly specify coverage report format. --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 99ca229c..c1043efc 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -34,7 +34,7 @@ jobs: python -m pip install --upgrade pip poetry poetry install --extras docs - name: Unit-tests - run: poetry run pytest -v --cov=mdbenchmark + run: poetry run pytest -v --cov=mdbenchmark --cov-report=xml - name: Upload coverage uses: codecov/codecov-action@v3 with: From c4eb9b871fe463482c0da8b6eb7b7162d9cbf7df Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 14:13:50 +0100 Subject: [PATCH 06/13] Add format and style checks. --- .github/workflows/tests.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c1043efc..07b73207 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -33,6 +33,14 @@ jobs: run: | python -m pip install --upgrade pip poetry poetry install --extras docs + - name: Check reformat + run: poetry run make reformat-check + - name: Check style + run: poetry run make flake8 + - name: Check sort + run: poetry run make isort-check + - name: Check reStructuredText + run: poetry run make rst-lint - name: Unit-tests run: poetry run pytest -v --cov=mdbenchmark --cov-report=xml - name: Upload coverage From d667c272947ab7958ab644becfd71d6ae022bd4a Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 14:29:14 +0100 Subject: [PATCH 07/13] Remove travis related files. --- .travis.yml | 77 ---------------------------------------- .travis/before_script.sh | 5 --- 2 files changed, 82 deletions(-) delete mode 100644 .travis.yml delete mode 100755 .travis/before_script.sh diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 4598e800..00000000 --- a/.travis.yml +++ /dev/null @@ -1,77 +0,0 @@ -os: linux -language: python -python: "3.8" - -branches: - only: - - develop - - master - - version-3 - -cache: - - pip: true - - directories: - - $PIP_CACHE_DIR - -env: - global: - - PIP_CACHE_DIR=$HOME/.cache/pip - - CODECOV="" - - PYTEST_COV="" - - UPGRADE_PIP="pip install --upgrade pip" - -jobs: - include: - - stage: "Linux - Unit tests" - name: "Python 3.8" - env: - - CODECOV="--cov mdbenchmark" - - PYTEST_COV="pytest-cov codecov" - - name: "Python 3.7" - language: python - python: "3.7" - - name: "Python 3.6" - language: python - python: "3.6" - dist: xenial - - - stage: "Linting and formatting" - name: "Formatting with black" - script: poetry run make reformat-check - - name: "Linting with flake8" - script: poetry run make flake8 - - name: "Sorting with isort" - script: poetry run make isort-check - - name: "Lint reStructuredText" - script: poetry run make rst-lint - - name: "Try to build documentation" - install: poetry install --extras docs - script: - - cd docs - - poetry run make build - - - stage: "macOS - Unit tests" - os: osx - osx_image: xcode11.2 - language: shell - before_script: - - bash .travis/before_script.sh - before_cache: - - rm -f "$HOME/Library/Caches/pip/log/debug.log" - cache: - directories: - - "$HOME/Library/Caches/pip" - - "$HOME/Library/Caches/pypoetry" - -before_install: - - $UPGRADE_PIP - - pip install poetry - -install: - - poetry install - -script: - - poetry run pytest $CODECOV - -after_success: - - if [ -z ${CODECOV} ]; then echo "Skipping codecov submit"; else codecov; fi diff --git a/.travis/before_script.sh b/.travis/before_script.sh deleted file mode 100755 index e91a2861..00000000 --- a/.travis/before_script.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash -set -euo pipefail - -mkdir -p $HOME/.matplotlib -echo "backend: TkAgg" > $HOME/.matplotlib/matplotlibrc From 063fdb06eb4fd9ba8883bf3714467194e8b19e3a Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Mon, 23 Jan 2023 15:50:08 +0100 Subject: [PATCH 08/13] Cleanup workflow. --- .github/workflows/tests.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 07b73207..d74fc156 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -30,9 +30,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'poetry' - name: Install mdbenchmark - run: | - python -m pip install --upgrade pip poetry - poetry install --extras docs + run: poetry install --extras docs - name: Check reformat run: poetry run make reformat-check - name: Check style From dc886b478be450e876ca06b3410201394c862785 Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Tue, 24 Jan 2023 10:25:22 +0100 Subject: [PATCH 09/13] Change badge from travis to gh-actions. --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 1ee2011a..aa40aa7a 100644 --- a/README.rst +++ b/README.rst @@ -11,8 +11,8 @@ Benchmark molecular dynamics simulations .. image:: https://img.shields.io/pypi/l/mdbenchmark.svg :target: https://pypi.python.org/pypi/mdbenchmark -.. image:: https://travis-ci.org/bio-phys/MDBenchmark.svg?branch=develop - :target: https://travis-ci.org/bio-phys/MDBenchmark +.. image:: https://github.com/bio-phys/MDBenchmark/actions/workflows/tests.yml/badge.svg?branch=develop + :target: https://github.com/bio-phys/MDBenchmark/actions/workflows/tests.yml .. image:: https://readthedocs.org/projects/mdbenchmark/badge/?version=latest&style=flat :target: https://mdbenchmark.readthedocs.io/en/latest/ From 25eae9827e8398c82189638ccc14fa1f4e6eb865 Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Tue, 24 Jan 2023 09:11:42 +0100 Subject: [PATCH 10/13] Add build test. --- .github/workflows/tests.yml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d74fc156..d150e4e8 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -46,8 +46,43 @@ jobs: with: env_vars: PYTHON fail_ci_if_error: true + - name: Build distribution + run: poetry build + - name: Upload build artifacts + uses: actions/upload-artifact@v3 + with: + name: dists.${{ matrix.python-version }} + path: dist/ - name: Make docs run: | cd docs poetry run make build + test-build: + + runs-on: ubuntu-latest + needs: test + strategy: + matrix: + python-version: ["3.7", "3.8"] + + steps: + - name: Enable pip-caching + run: touch requirements.txt + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: 'pip' + - name: Update pip + run: pip install --upgrade pip + - name: Download build artifacts + uses: actions/download-artifact@v3 + with: + name: dists.${{ matrix.python-version }} + path: dist + - name: Install mdbenchmark + run: pip install dist/*.tar.gz + - name: Check run + run: mdbenchmark + From 1b457ce3718be20782e5db541ae0979d21e03730 Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Tue, 24 Jan 2023 11:32:33 +0100 Subject: [PATCH 11/13] Make comment on pip-cache not working. --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d150e4e8..879ab73d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -73,7 +73,7 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - cache: 'pip' + cache: 'pip' #doesn't seem to work - name: Update pip run: pip install --upgrade pip - name: Download build artifacts From 0beef7e9a19ac1b5ce7dd2b3b0f8e4a27f9c98e2 Mon Sep 17 00:00:00 2001 From: ksebaz <58634313+ksebaz@users.noreply.github.com> Date: Wed, 25 Jan 2023 16:37:50 +0100 Subject: [PATCH 12/13] Pin markupsafe dependency. This fixes an incompatibility with the jinja2 ^2.10 capping that leads to the use of an unsupported jinja2 version that is incompatible the resolved markupsafe. --- poetry.lock | 2447 ++++++++++++++++++++++++++++-------------------- pyproject.toml | 1 + 2 files changed, 1428 insertions(+), 1020 deletions(-) diff --git a/poetry.lock b/poetry.lock index ea93a8c9..03cc3999 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,120 +1,151 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + [[package]] -category = "main" -description = "A configurable sidebar-enabled Sphinx theme" name = "alabaster" +version = "0.7.13" +description = "A configurable sidebar-enabled Sphinx theme" +category = "main" optional = true -python-versions = "*" -version = "0.7.12" - -[[package]] -category = "dev" -description = "apipkg: namespace control and lazy-import mechanism" -name = "apipkg" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.5" +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] [[package]] -category = "dev" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -marker = "python_version >= \"3.6\" and python_version < \"4.0\"" name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "dev" optional = false python-versions = "*" -version = "1.4.4" +files = [ + {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, + {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, +] [[package]] -category = "dev" -description = "Disable App Nap on OS X 10.9" -marker = "sys_platform == \"darwin\"" name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "dev" optional = false python-versions = "*" -version = "0.1.0" +files = [ + {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, + {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, +] [[package]] -category = "main" -description = "An unobtrusive argparse wrapper with natural syntax" name = "argh" +version = "0.26.2" +description = "An unobtrusive argparse wrapper with natural syntax" +category = "main" optional = true python-versions = "*" -version = "0.26.2" +files = [ + {file = "argh-0.26.2-py2.py3-none-any.whl", hash = "sha256:a9b3aaa1904eeb78e32394cd46c6f37ac0fb4af6dc488daa58971bdc7d7fcaf3"}, + {file = "argh-0.26.2.tar.gz", hash = "sha256:e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65"}, +] [[package]] -category = "main" -description = "Draws ASCII trees." name = "asciitree" +version = "0.3.3" +description = "Draws ASCII trees." +category = "main" optional = false python-versions = "*" -version = "0.3.3" +files = [ + {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"}, +] [[package]] -category = "dev" -description = "An abstract syntax tree for Python with inference support." name = "astroid" +version = "2.9.0" +description = "An abstract syntax tree for Python with inference support." +category = "dev" optional = false -python-versions = ">=3.5" -version = "2.4.2" +python-versions = "~=3.6" +files = [ + {file = "astroid-2.9.0-py3-none-any.whl", hash = "sha256:776ca0b748b4ad69c00bfe0fff38fa2d21c338e12c84aa9715ee0d473c422778"}, + {file = "astroid-2.9.0.tar.gz", hash = "sha256:5939cf55de24b92bda00345d4d0659d01b3c7dafb5055165c330bc7c568ba273"}, +] [package.dependencies] -lazy-object-proxy = ">=1.4.0,<1.5.0" -six = ">=1.12,<2.0" -wrapt = ">=1.11,<2.0" - 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Add test for python 3.9. --- .github/workflows/tests.yml | 4 ++-- pyproject.toml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 879ab73d..133668c0 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -16,7 +16,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.7", "3.8"] + python-version: ["3.7", "3.8", "3.9"] env: PYTHON: ${{ matrix.python-version }} @@ -64,7 +64,7 @@ jobs: needs: test strategy: matrix: - python-version: ["3.7", "3.8"] + python-version: ["3.7", "3.8", "3.9"] steps: - name: Enable pip-caching diff --git a/pyproject.toml b/pyproject.toml index 84a83db0..2fd38de4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,9 +21,9 @@ classifiers = [ "Operating System :: POSIX", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", @@ -32,7 +32,7 @@ classifiers = [ ] [tool.poetry.dependencies] -python = "^3.6" +python = "^3.7" numpy = ">=1.15" pandas = ">=0.24" matplotlib = ">=2"