Rename .drone.yml to .woodpecker.yaml

.github/workflows/lint_python.yml

@@ -20,6 +20,7 @@ jobs:
  - run: flake8 . --count --exit-zero --max-complexity=66 --max-line-length=118
  --show-source --statistics
  - run: isort --check-only --profile black . || true
+ - run: pip install setuptools
  - run: pip install --editable . || pip install .
  - run: mkdir --parents --verbose .mypy_cache
  - run: mypy --ignore-missing-imports --install-types --non-interactive . || true

.drone.yml → .woodpecker.yaml

@@ -1,16 +1,18 @@
-pipeline:
- restore-cache:
- image: drillster/drone-volume-cache
- restore: true
- mount:
- - ./cache-ci/pyusrb
- - ./cache-ci/conda_packages
- - ./cache-ci/pip_cache
- volumes:
- - /tmp/cache:/cache
- ttl: 90 # liftetime in days
+when:
+ - event: [pull_request, tag, cron, push]
 
- install:
+steps:
+
+ - name: restore-cache
+ image: bjodah/bjodahimg20dot:21.8.a
+ commands:
+ - curl ftp://chempy:$${ARTIFACTS_PASS}@$${FTP_SERVER}/cache/cache-ci.tar | tar x
+ secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
+ when:
+ - event: push
+ repo: bjodah/chempy
+
+ - name: install
  image: bjodah/bjodahimg20dot:21.8.a
  environment:
  - CC=gcc-11
@@ -30,12 +32,11 @@ pipeline:
  - git fetch -tq
  - python3 setup.py sdist # test pip installable sdist (checks MANIFEST.in)
  - git archive -o dist/chempy-head.zip HEAD # test pip installable zip (symlinks break)
- - mkdir -p deploy/public_html/branches/${DRONE_BRANCH}
- - cp dist/chempy-* deploy/public_html/branches/${DRONE_BRANCH}/
+ - mkdir -p deploy/public_html/branches/${CI_COMMIT_BRANCH}
+ - cp dist/chempy-* deploy/public_html/branches/${CI_COMMIT_BRANCH}/
 
- test-suite:
+ - name: test-suite
  image: bjodah/bjodahimg20dot:21.8.a
- group: testing
  environment:
  - CC=gcc-11
  - CXX=g++-11
@@ -52,19 +53,20 @@ pipeline:
  - bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
  - ./scripts/run_tests.sh --cov chempy --cov-report html
  - ./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
- - cp -r htmlcov/ deploy/public_html/branches/${DRONE_BRANCH}/
+ - cp -r htmlcov/ deploy/public_html/branches/${CI_COMMIT_BRANCH}/
  - ./.ci/grep-for-merge-blocking-token.sh
  - export CHEMPY_DEPRECATION_FILTER=ignore
  - python3 -m virtualenv /tmp/test_sdist
  - python3 -m virtualenv /tmp/test_git_archive
- - cd deploy/public_html/branches/${DRONE_BRANCH}
+ - cd deploy/public_html/branches/${CI_COMMIT_BRANCH}
  - unset CHEMPY_SKIP_NO_TESTS # I can't get pip to install extras when using local file...
  - bash -c "source /tmp/test_sdist/bin/activate; pip install --cache-dir $CACHE_ROOT/pip_cache file://$(realpath $(eval ls chempy-*.tar.gz))#chempy[all] pytest; pytest --pyargs chempy"
  - bash -c "source /tmp/test_git_archive/bin/activate; pip install --cache-dir $CACHE_ROOT/pip_cache file://$(realpath chempy-head.zip)#chempy[all] pytest; pytest --pyargs chempy"
+ depends_on:
+ - install
 
- render-notebooks:
+ - name: render-notebooks
  image: bjodah/bjodahimg20dot:21.8.a
- group: testing
  environment:
  - CHEMPY_DEPRECATION_FILTER=ignore
  - SUNDBASE=/opt/sundials-5.7.0-release
@@ -79,20 +81,11 @@ pipeline:
  - ./scripts/render_notebooks.sh
  - ./.ci/grep-for-binary-data.sh
  - mv index.html index.ipynb.html
-# - (cd examples/; for f in bokeh_*.py; do python3 -m bokeh html $f; done)
- - cp -r index.* examples/ "deploy/public_html/branches/${DRONE_BRANCH}"
-
-# conda-recipe:
-# image: bjodah/bjodahimg20dot:21.8.a
-# group: testing
-# commands:
-# - export CONDA_PKGS_DIRS=$(pwd)/cache-ci/conda_packages
-# - git fetch -tq
-# - PATH=/opt/miniconda3/bin:$PATH conda config --add channels bjodah # sym, pyodesys, pyneqsys
-# - PATH=/opt/miniconda3/bin:$PATH conda build --output-folder "deploy/public_html/branches/${DRONE_BRANCH}" conda-recipe
-# - (cd $CONDA_PKGS_DIRS; find . -maxdepth 1 -type d -not -path . -not -path .. | xargs rm -r)
+ - cp -r index.* examples/ "deploy/public_html/branches/${CI_COMMIT_BRANCH}"
+ depends_on:
+ - install
 
- compile-documentation:
+ - name: compile-documentation
  image: bjodah/bjodahimg20dot:21.8.a
  environment:
  - CHEMPY_DEPRECATION_FILTER=ignore
@@ -104,26 +97,34 @@ pipeline:
  - export LD_LIBRARY_PATH=$SUNDBASE/lib
  - ./scripts/generate_docs.sh
  - cp LICENSE doc/_build/html/
- - cp -r doc/_build/html/ deploy/public_html/branches/${DRONE_BRANCH}
+ - cp -r doc/_build/html/ deploy/public_html/branches/${CI_COMMIT_BRANCH}
+ depends_on:
+ - test-suite
+ - render-notebooks
 
- rebuild-cache:
- image: drillster/drone-volume-cache
- rebuild: true
- mount:
-# - ./cache-ci/sund-3.2.1
- - ./cache-ci/pyusrb
- - ./cache-ci/conda_packages
- - ./cache-ci/pip_cache
- volumes:
- - /tmp/cache:/cache
+ - name: rebuild-cache
+ image: bjodah/bjodahimg20dot:21.8.a
+ commands:
+ - find ./cache-ci/ -type f -mtime +90 -exec rm {} \;
+ - tar cf cache-ci.tar ./cache-ci/
+ - curl -T cache-ci.tar ftp://chempy:$${ARTIFACTS_PASS}@$${FTP_SERVER}/cache/
+ secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
+ when:
+ - event: push
+ repo: bjodah/chempy
+ depends_on:
+ - compile-documentation
 
- deploy:
- image: drillster/drone-rsync
+ - name: deploy-public-html
+ image: bjodah/bjodahimg20dot:21.8.a
+ commands:
+ - tar czf chempy-${CI_COMMIT_BRANCH}.tar.gz ./deploy/public_html
+ - curl -T chempy-${CI_COMMIT_BRANCH}.tar.gz ftp://chempy:$${ARTIFACTS_PASS}@$${FTP_SERVER}/public_html/
+ secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
  when:
- event: [push]
- hosts: [ "hera.physchem.kth.se" ]
- port: 22
- user: chempy
- secrets: [ rsync_key ] # secret only set fro event "push" not "pull_request"
- source: ./deploy/public_html
- target: ~/
+ - event: push
+ repo: bjodah/chempy
+ depends_on:
+ - compile-documentation
+
+

chempy/chemistry.py

@@ -456,9 +456,8 @@ def _init_stoich(container):
  if isinstance(container, set):
  container = {k: 1 for k in container}
  container = container or {}
- if (
- type(container) == dict
- ): # we don't want isinstance here in case of OrderedDict
+ if type(container) == dict: # noqa
+ # we don't want isinstance here in case of OrderedDict
  container = OrderedDict(sorted(container.items(), key=lambda kv: kv[0]))
  return container
 
@@ -1456,11 +1455,10 @@ def balance_stoichiometry(
  substances = OrderedDict(
  [(k, substance_factory(k)) for k in substances.split()]
  )
- if (
- type(reactants) == set
- ): # we don't want isinstance since it might be "OrderedSet"
+ if type(reactants) == set: # noqa
+ # we don't want isinstance since it might be "OrderedSet"
  reactants = sorted(reactants)
- if type(products) == set:
+ if type(products) == set: # noqa
  products = sorted(products)
  subst_keys = list(reactants) + list(products)
 

examples/protein_binding_unfolding_4state_model.ipynb

@@ -209,7 +209,7 @@
  "source": [
  "Try hovering over the names to have them highlighted (this is particularly useful when working with large reaction sets).\n",
  "\n",
- "We ca also generate tables representing the unimolecular reactions involing each substance, or the matrix showing the bimolecular reactions:"
+ "We ca also generate tables representing the unimolecular reactions involving each substance, or the matrix showing the bimolecular reactions:"
  ]
  },
  {