Merge branch 'nov20' of github.com:bjodah/chempy into nov20

.github/workflows/lint_python.yml

@@ -0,0 +1,29 @@
+name: lint_python
+on: [pull_request, push]
+jobs:
+  lint_python:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: pip install --upgrade pip wheel
+      - run: pip install bandit "black[jupyter]" codespell flake8 flake8-2020 
+                         isort mypy pytest pyupgrade
+      - run: bandit --recursive --skip B101,B102,B110,B112,B307,B404,B603,B607 .
+      - run: black --check . || true
+      - run: codespell --ignore-words-list="ans,claus,fith,nam,nd,ond,serie,te"
+      - run: flake8 . --count --max-complexity=66 --max-line-length=118
+                      --show-source --statistics
+      - run: pip install flake8-bugbear flake8-comprehensions flake8-return flake8-simplify
+      - 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
+      - run: pytest .
+      - run: pytest --doctest-modules .
+      - run: shopt -s globstar && pyupgrade --py37-plus **/*.py || true

.drone.yml → .woodpecker.yaml

@@ -1,17 +1,19 @@
-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:
-    image: bjodah/bjodahimg20dot:21.7.c
+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
       - CXX=g++-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:
-    image: bjodah/bjodahimg20dot:21.7.c
-    group: testing
+  - name: test-suite
+    image: bjodah/bjodahimg20dot:21.8.a
     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:
-    image: bjodah/bjodahimg20dot:21.7.c
-    group: testing
+  - name: render-notebooks
+    image: bjodah/bjodahimg20dot:21.8.a
     environment:
       - CHEMPY_DEPRECATION_FILTER=ignore
       - SUNDBASE=/opt/sundials-5.7.0-release
@@ -79,21 +81,12 @@ 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:21.7.c
-#    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:
-    image: bjodah/bjodahimg20dot:21.7.c
+  - name: compile-documentation
+    image: bjodah/bjodahimg20dot:21.8.a
     environment:
       - CHEMPY_DEPRECATION_FILTER=ignore
       - SUNDBASE=/opt/sundials-5.7.0-release
@@ -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

@@ -426,7 +426,8 @@ 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
 
@@ -1275,10 +1276,13 @@ def balance_stoichiometry(reactants, products, substances=None,
     if substances is None:
         substances = OrderedDict([(k, substance_factory(k)) for k in chain(reactants, products)])
     if isinstance(substances, str):
-        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"
+        substances = OrderedDict(
+            [(k, substance_factory(k)) for k in substances.split()]
+        )
+    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)
 

chempy/kinetics/rates.py

@@ -198,8 +198,9 @@ def heaviside(x, z):
         elif hasattr(backend, 'clip'):  # e.g. numpy
             def heaviside(x, z):
                 assert z == 0
-                lx = backend.log(backend.maximum(x, tiny))
-                xclp = be.clip(lx, lo, hi)
+                lx = backend.log(backend.maximum(backend.array(x), tiny))
+                xclp = backend.clip(lx, lo, hi)
+                x = (xclp - lo)/(hi - lo)
                 y = (3 - 2*x)*x*x
                 return y
         else:

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:"
    ]
   },
   {