Merge branch 'master' of github.com:bjodah/chempy

Author: bjodah

.ci/_source_common_env.sh

@@ -0,0 +1,8 @@
+export CACHE_ROOT=$(pwd)/cache-ci
+export PYTHONUSERBASE=$CACHE_ROOT/pyusrb
+export CPATH=$SUNDIALS_ROOT/include:/usr/include/suitesparse:${CPATH:-}  # sunlinsol_klu.h includes "klu.h"
+export CPLUS_INCLUDE_PATH=${Boost_ROOT}/include
+export LIBRARY_PATH=$SUNDIALS_ROOT/lib
+export LD_LIBRARY_PATH=$SUNDIALS_ROOT/lib
+
+source $(compgen -G "/opt-3/cpython-v3.*-apt-deb/bin/activate")

.ci/run-01-install-deps-create-sdist.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+set -euxo pipefail
+. .ci/_source_common_env.sh
+if [ ! -d $PYTHONUSERBASE ]; then mkdir -p $PYTHONUSERBASE; fi
+
+python -m pip install --cache-dir $CACHE_ROOT/pip_cache --upgrade-strategy=eager --upgrade cython
+python -m pip install --cache-dir $CACHE_ROOT/pip_cache -e .[all]
+python -c "import pycvodes; import pyodesys; import pygslodeiv2"  # debug this CI config
+git fetch -tq
+#python setup.py sdist                    # test pip installable sdist (checks MANIFEST.in)
+python -m build --sdist                    # test pip installable sdist (checks MANIFEST.in)
+git archive -o dist/chempy-head.zip HEAD  # test pip installable zip (symlinks break)

.ci/run-02-test-suite.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+set -euxo pipefail
+. .ci/_source_common_env.sh
+
+bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
+./scripts/run_tests.sh --cov chempy --cov-report html
+./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
+cp -r htmlcov/ dist/*.* deploy/public_html/branches/${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/${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"

.ci/run-03-render-notebooks.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -euxo pipefail
+. .ci/_source_common_env.sh
+
+./scripts/render_notebooks.sh
+mv index.html index.ipynb.html
+cp -r index.* examples/ "deploy/public_html/branches/${CI_COMMIT_BRANCH}"

.woodpecker.yaml

@@ -1,110 +1,58 @@
+variables:
+#   Developers are not expected to actually use this CI image locally, however,
+#   using this image avoid downloading a bunch of PyPI packages for each CI run.
+  - &ci_image 'cont-reg.bjodah.se:443/bjodah/triceratops-6:32'
+
 when:
-  - event: [pull_request, tag, cron, push]
+  - event: [push]
 
 steps:
 
   - name: restore-cache
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     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
+  - name: test-suite
+    image: *ci_image
     environment:
-      - CC=gcc-11
-      - CXX=g++-11
-      - CPLUS_INCLUDE_PATH=/opt/boost-1.77.0/include
-      - SUNDBASE=/opt/sundials-5.7.0-release
-      - CPATH=/usr/include/suitesparse  # sunlinsol_klu.h includes "klu.h"
+      - CHEMPY_SKIP_NO_TESTS=1
     commands:
-      - export CACHE_ROOT=$(pwd)/cache-ci
-      - export PYTHONUSERBASE=$CACHE_ROOT/pyusrb
-      - if [ ! -d $PYTHONUSERBASE ]; then mkdir -p $PYTHONUSERBASE; fi
-      - export CPATH=$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 $CACHE_ROOT/pip_cache --user -e .[all]
-      - python3 -c "import pycvodes; import pyodesys; import pygslodeiv2"  # debug this CI config
-      - git fetch -tq
-      - python3 setup.py sdist                    # test pip installable sdist (checks MANIFEST.in)
-      - git archive -o dist/chempy-head.zip HEAD  # test pip installable zip (symlinks break)
+      - mkdir -p deploy/public_html/branches/${CI_COMMIT_BRANCH}/
+      - bash -l .ci/run-01-install-deps-create-sdist.sh
+      - bash -l .ci/run-02-test-suite.sh
       - mkdir -p deploy/public_html/branches/${CI_COMMIT_BRANCH}
       - cp dist/chempy-* deploy/public_html/branches/${CI_COMMIT_BRANCH}/
 
-  - name: test-suite
-    image: bjodah/bjodahimg20dot:21.8.a
-    environment:
-      - CC=gcc-11
-      - CXX=g++-11
-      - CPLUS_INCLUDE_PATH=/opt/boost-1.77.0/include
-      - SUNDBASE=/opt/sundials-5.7.0-release
-      - CPATH=/usr/include/suitesparse  # sunlinsol_klu.h includes "klu.h"
-      - CHEMPY_SKIP_NO_TESTS=1
-    commands:
-      - export CACHE_ROOT=$(pwd)/cache-ci
-      - export PYTHONUSERBASE=$CACHE_ROOT/pyusrb
-      - export CPATH=$SUNDBASE/include:$CPATH
-      - export LIBRARY_PATH=$SUNDBASE/lib
-      - export LD_LIBRARY_PATH=$SUNDBASE/lib
-      - bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
-      - ./scripts/run_tests.sh --cov chempy --cov-report html
-      - ./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
-      - cp -r htmlcov/ deploy/public_html/branches/${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/${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
 
   - name: render-notebooks
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     environment:
       - CHEMPY_DEPRECATION_FILTER=ignore
-      - SUNDBASE=/opt/sundials-5.7.0-release
-      - CC=gcc-11
-      - CXX=g++-11
-      - CPATH=/usr/include/suitesparse  # sunlinsol_klu.h includes "klu.h"
     commands:
-      - export PYTHONUSERBASE=$(pwd)/cache-ci/pyusrb
-      - export CPATH=$SUNDBASE/include:$CPATH
-      - export LIBRARY_PATH=$SUNDBASE/lib
-      - export LD_LIBRARY_PATH=$SUNDBASE/lib
-      - ./scripts/render_notebooks.sh
-      - ./.ci/grep-for-binary-data.sh
-      - mv index.html index.ipynb.html
-      - cp -r index.* examples/ "deploy/public_html/branches/${CI_COMMIT_BRANCH}"
-    depends_on:
-      - install
+      - mkdir -p deploy/public_html/branches/${CI_COMMIT_BRANCH}/
+      - bash -l .ci/run-01-install-deps-create-sdist.sh
+      - bash -l .ci/run-03-render-notebooks.sh
+      - .ci/grep-for-binary-data.sh
 
   - name: compile-documentation
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     environment:
       - CHEMPY_DEPRECATION_FILTER=ignore
-      - SUNDBASE=/opt/sundials-5.7.0-release
     commands:
-      - export PYTHONUSERBASE=$(pwd)/cache-ci/pyusrb
-      - export CPATH=$SUNDBASE/include
-      - export LIBRARY_PATH=$SUNDBASE/lib
-      - export LD_LIBRARY_PATH=$SUNDBASE/lib
-      - ./scripts/generate_docs.sh
+      - bash -lc '. .ci/_source_common_env.sh; ./scripts/generate_docs.sh'
       - cp LICENSE doc/_build/html/
       - cp -r doc/_build/html/ deploy/public_html/branches/${CI_COMMIT_BRANCH}
     depends_on:
       - test-suite
       - render-notebooks
 
   - name: rebuild-cache
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     commands:
       - find ./cache-ci/ -type f -mtime +90 -exec rm {} \;
       - tar cf cache-ci.tar ./cache-ci/
@@ -117,7 +65,7 @@ steps:
       - compile-documentation
 
   - name: deploy-public-html
-    image: bjodah/bjodahimg20dot:21.8.a
+    image: *ci_image
     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/
@@ -127,5 +75,3 @@ steps:
        repo: bjodah/chempy
     depends_on:
       - compile-documentation
-
-

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2018, Björn Dahlgren
+Copyright (c) 2015-2025, Björn Dahlgren
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

README.rst

@@ -236,13 +236,13 @@ example of how ChemPy can check consistency of units:
 .. code:: python
 
    >>> from chempy import Reaction
-   >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4/M/s")
+   >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4/M/s")  # DOCTEST: +ELLIPSIS
    Traceback (most recent call last):
    ...
-   ValueError: Unable to convert between units of "1/M" and "dimensionless"
+   ValueError: Incompatible units
    >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4/s")
    >>> from chempy.units import to_unitless, default_units as u
-   >>> to_unitless(r.param, 1/u.minute)
+   >>> to_unitless(r.param, 1/u.minute).item()
    0.006
 
 right now the ``.units`` module wraps the quantities_ package with some minor

chempy/__init__.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""
-ChemPy is a Python package useful for solving problems in chemistry.
-"""
+"""ChemPy is a Python package useful for solving problems in chemistry."""
 
 
 from ._url import __url__

chempy/_solution.py

@@ -8,12 +8,12 @@
 >>> s1 = Solution(0.1*u.dm3, {'CH3OH': 0.1 * u.molar})
 >>> s2 = Solution(0.3*u.dm3, {'CH3OH': 0.4 * u.molar, 'Na+': 2e-3*u.molar, 'Cl-': 2e-3*u.molar})
 >>> s3 = s1 + s2
->>> abs(to_unitless(s3.volume - 4e-4 * u.m**3, u.dm3)) < 1e-15
+>>> bool(abs(to_unitless(s3.volume - 4e-4 * u.m**3, u.dm3)) < 1e-15)
 True
 >>> s3.concentrations.isclose({'CH3OH': 0.325*u.molar, 'Na+': 1.5e-3*u.molar, 'Cl-': 1.5e-3*u.molar})
 True
 >>> s4 = s3.dissolve({'CH3OH': 1*u.gram})
->>> abs(s4.concentrations['CH3OH'] - (0.325 + 1/(12.011 + 4*1.008 + 15.999)/.4)*u.molar) < 1e-4
+>>> bool(abs(s4.concentrations['CH3OH'] - (0.325 + 1/(12.011 + 4*1.008 + 15.999)/.4)*u.molar) < 1e-4)
 True
 
 """

chempy/chemistry.py

@@ -517,15 +517,15 @@ def from_string(cls, string, substance_keys=None, globals_=None, **kwargs):
         True
         >>> r3 = Reaction.from_string("A -> B; 1/second", 'A B')
         >>> from chempy.units import to_unitless, default_units as u
-        >>> to_unitless(r3.param, u.hour**-1)
+        >>> to_unitless(r3.param, u.hour**-1).item()
         3600.0
         >>> r4 = Reaction.from_string("A -> 2 B; 'k'", 'A B')
         >>> r4.rate(dict(A=3, B=5, k=7)) == {'A': -3*7, 'B': 2*3*7}
         True
-        >>> r5 = Reaction.from_string("A -> B; 1/molar/second", 'A B')
+        >>> r5 = Reaction.from_string("A -> B; 1/molar/second", 'A B')  # DOCTEST: +ELLIPSIS
         Traceback (most recent call last):
             ...
-        ValueError: Unable to convert between units ...
+        ValueError: Incompatible units
 
 
         Notes