Merge branch 'master' into HEAD

.github/workflows/lint_python.yml

@@ -17,12 +17,14 @@ jobs:
       - 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
+      - run: flake8 . --count --max-complexity=66 --max-line-length=129
                       --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
+      - run: flake8 . --count --exit-zero --max-complexity=66 --max-line-length=129
                       --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: shopt -s globstar && pyupgrade --py37-plus **/*.py || 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
@@ -25,17 +27,17 @@ pipeline:
       - export CPATH=$SUNDBASE/include:$CPATH
       - export LIBRARY_PATH=$SUNDBASE/lib
       - export LD_LIBRARY_PATH=$SUNDBASE/lib
+      - python3 -m pip install --cache-dir $CACHE_ROOT/pip_cache --user --upgrade-strategy=eager --upgrade cython
       - python3 -m pip install --cache-dir $CACHE_ROOT/pip_cache --user -e .[all]
       - python3 -c "import pycvodes; import pyodesys; import pygslodeiv2"  # debug this CI config
       - git fetch -tq
       - python3 setup.py sdist                    # test pip installable sdist (checks MANIFEST.in)
       - git archive -o dist/chempy-head.zip HEAD  # test pip installable zip (symlinks break)
-      - mkdir -p deploy/public_html/branches/${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 +54,20 @@ 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 +82,11 @@ 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 +98,34 @@ 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
+
+

README.rst

@@ -3,13 +3,13 @@ ChemPy
 
 .. image:: https://github.com/bjodah/chempy/actions/workflows/lint_python.yml/badge.svg
    :target: https://github.com/bjodah/chempy/actions/workflows/lint_python.yml
-   :alt: Build status
+   :alt: Github Actions CI status
+.. image:: https://hackspett.bjodah.se/api/badges/1/status.svg
+   :target: https://hackspett.bjodah.se/repos/1
+   :alt: Woodpecker CI status
 .. image:: https://img.shields.io/pypi/v/chempy.svg
    :target: https://pypi.python.org/pypi/chempy
    :alt: PyPI version
-.. image:: https://img.shields.io/badge/python-3.8,3.9-blue.svg
-   :target: https://www.python.org/
-   :alt: Python version
 .. image:: https://img.shields.io/pypi/l/chempy.svg
    :target: https://github.com/bjodah/chempy/blob/master/LICENSE
    :alt: License
@@ -374,16 +374,6 @@ literature with relevance in chemistry. Here is how you use one of these formula
    [H2O] = 55.18 M (at 35 °C)
 
 
-Run notebooks using binder
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-Using only a web-browser (and an internet connection) it is possible to explore the
-notebooks here: (by the courtesy of the people behind mybinder)
-
-.. image:: http://mybinder.org/badge.svg
-   :target: https://mybinder.org/v2/gh/bjodah/chempy/f5f2546e79e165ba8fb258fc87d83a7fbdcbad64?filepath=index.ipynb
-   :alt: Binder
-
-
 Citing
 ------
 If you make use of ChemPy in e.g. academic work you may cite the following peer-reviewed publication:
@@ -395,7 +385,7 @@ If you make use of ChemPy in e.g. academic work you may cite the following peer-
 Depending on what underlying solver you are using you should also cite the appropriate paper
 (you can look at the list of references in the JOSS article). If you need to reference,
 in addition to the paper, a specific point version of ChemPy (for e.g. reproducibility)
-you can get per-version DOIs from the zendodo archive:
+you can get per-version DOIs from the zenodo archive:
 
 .. image:: https://zenodo.org/badge/8840/bjodah/chempy.svg
    :target: https://zenodo.org/badge/latestdoi/8840/bjodah/chempy

chempy/_release.py

@@ -1 +1 @@
-__version__ = "0.8.1.dev0+git"
+__version__ = "0.9.0.dev0+git"

chempy/chemistry.py

@@ -98,6 +98,16 @@ def __eq__(self, other):
                 return False
         return True
 
+    def __hash__(self) -> int:
+        hashed_values = []
+        for key in self.attrs:
+            value = getattr(self, key)
+            if isinstance(value, dict):
+                hashed_values.append(hash(tuple(sorted(value.items()))))
+            else:
+                hashed_values.append(hash(value))
+        return sum(hashed_values)
+
     @property
     def charge(self):
         """Convenience property for accessing ``composition[0]``"""
@@ -446,9 +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
 
@@ -1446,11 +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)
 

chempy/tests/test_chemistry.py

@@ -40,6 +40,8 @@ def test_Substance():
     assert s.composition == {0: 1, 1: 1}
     assert s.charge == 1
     assert abs(s.mass - 1.008) < 1e-3
+    assert s in {s: 1}
+    assert hash(s) != hash(Substance.from_formula("He"))
 
 
 def test_Substance__2():

chempy/util/parsing.py

@@ -95,7 +95,7 @@ def _get_formula_parser():
                  | '{' formula '}'
                  | '[' formula ']' ) count prime charge?
         formula :: term+
-        hydrate :: '.' count? formula
+        hydrate :: ( '..' | '\u00B7' ) count? formula
         state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
         compound :: count formula hydrate? state?
 
@@ -114,7 +114,7 @@ def _get_formula_parser():
                  | '{' formula '}'
                  | '[' formula ']' ) count prime charge?
         formula :: term+
-        hydrate :: '..' count? formula
+        hydrate :: ( '..' | '\u00B7' ) count? formula
         state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
         compound :: count formula hydrate? state?
     """
@@ -334,7 +334,7 @@ def _parse_stoich(stoich):
 
 _unicode_mapping = {k + "-": v + "-" for k, v in zip(_greek_letters, _greek_u)}
 _unicode_mapping["."] = "⋅"
-_unicode_infix_mapping = {"..": "·"}
+_unicode_infix_mapping = {"..": "\u00b7"}  # 0x00b7: '·'
 
 _html_mapping = {k + "-": "&" + k + ";-" for k in _greek_letters}
 _html_mapping["."] = "⋅"
@@ -379,14 +379,19 @@ def formula_to_composition(
     True
     >>> formula_to_composition('Na2CO3..7H2O') == {11: 2, 6: 1, 8: 10, 1: 14}
     True
+    >>> formula_to_composition('UO2.3') == {92: 1, 8: 2.3}
+    True
 
     """
     if prefixes is None:
         prefixes = _latex_mapping.keys()
 
     stoich_tok, chg_tok = _formula_to_parts(formula, prefixes, suffixes)[:2]
     tot_comp = {}
-    parts = stoich_tok.split("..")
+    if '\u00b7' in stoich_tok:
+        parts = stoich_tok.split('\u00b7')
+    else:
+        parts = stoich_tok.split("..")
 
     for idx, stoich in enumerate(parts):
         if idx == 0:
@@ -532,7 +537,10 @@ def _formula_to_format(
     suffixes=("(s)", "(l)", "(g)", "(aq)"),
 ):
     parts = _formula_to_parts(formula, prefixes.keys(), suffixes)
-    stoichs = parts[0].split("..")
+    if '\u00b7' in parts[0]:
+        stoichs = parts[0].split('\u00b7')
+    else:
+        stoichs = parts[0].split("..")
     string = ""
     for idx, stoich in enumerate(stoichs):
         if idx == 0:
@@ -600,9 +608,11 @@ def formula_to_latex(formula, prefixes=None, infixes=None, **kwargs):
     )
 
 
-_unicode_sub = {}
+_unicode_sub = {
+    ".": ".",
+}
 
-for k, v in enumerate("₀₁₂₃₄₅₆₇₈₉"):
+for k, v in enumerate("₀₁₂₃₄₅₆₇₈₉."):
     _unicode_sub[str(k)] = v
 
 _unicode_sup = {