Test from installed wheel

.github/workflows/test.yml

@@ -7,9 +7,44 @@ on:
     branches: [ master ]
 
 jobs:
-  test:
+  build-wheel:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Build the wheel
+      run: |
+        python -m pip install build
+        python -m build
+
+    - name: Upload wheel
+      uses: actions/upload-artifact@v4
+      with:
+        name: wheel
+        path: dist/*.whl
+
+    - name: Run the tests
+      run: |
+        python -m pip install numpy pyparsing pytest pytest-cov
+        pytest -v
+
+    - name: Build the docs
+      run: |
+        python -m pip install matplotlib sphinx
+        python -m pip install dist/periodictable*.whl
+        make -j 4 -C doc/sphinx SPHINXOPTS="-W --keep-going" html
 
+  # Test the wheel on different platforms
+  test:
     runs-on: ${{ matrix.cfg.os }}
+    needs: build-wheel
+
     strategy:
       matrix:
         cfg:
@@ -19,6 +54,7 @@ jobs:
           - { os: ubuntu-latest, py: 3.11, doc: 1 }
           - { os: windows-latest, py: 3.11 }
           - { os: macos-latest, py: 3.11 }
+      fail-fast: false
 
     steps:
     - uses: actions/checkout@v4
@@ -28,18 +64,24 @@ jobs:
       with:
         python-version: ${{ matrix.cfg.py }}
 
-    - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install wheel setuptools
-        python -m pip install numpy scipy matplotlib pytest pytest-cov
+    - name: Download the wheel
+      uses: actions/download-artifact@v4
+      with:
+        name: wheel
+        path: dist
+
+    - name: Install the wheel
+      run: python -m pip install dist/periodictable*.whl
+      shell: bash
 
-    - name: Test with pytest
+    - name: Install Python dependencies
       run: |
-        pytest -v
+        python -m pip install pytest pytest-cov
 
-    - name: check that the docs build (linux only)
-      if: matrix.cfg.doc == 1
+    # Change into the test directory to test the wheel so that the
+    # source directory is not on the path. Full tests with coverage are
+    # run before building the wheel.
+    - name: Test wheel with pytest
       run: |
-        python -m pip install sphinx
-        make -j 4 -C doc/sphinx SPHINXOPTS="-W --keep-going" html
+        cd test
+        pytest -v --pyargs --import-mode=append periodictable . ../doc/sphinx/guide

MANIFEST.in

@@ -1,8 +1,8 @@
 include LICENSE.txt
 include README.rst
-graft doc
 graft periodictable/xsf
 include periodictable/activation.dat
+prune doc
 prune doc/sphinx/_build
 prune doc/sphinx/build
 prune */__pycache__

doc/sphinx/Makefile

@@ -31,7 +31,7 @@ help:
 clean:
 	-rm -rf _build/* build/* plots/*.pyc plots/*.png
 
-html: build
+html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
 	@echo
 	@echo "Build finished. The HTML pages are in _build/html."
@@ -66,7 +66,7 @@ qthelp:
 	@echo "To view the help file:"
 	@echo "# assistant -collectionFile _build/qthelp/Periodic Table.qhc"
 
-latex: build
+latex:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in _build/latex."
@@ -92,5 +92,3 @@ doctest:
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in _build/doctest/output.txt."
 
-build:
-	cd ../.. && python setup.py build

doc/sphinx/guide/extending.rst

@@ -25,7 +25,7 @@ The simplest solution is to load it directly when your package is imported.
 In the current example, this could be done by adding the following
 line to the end of the file::
 
-    init(periodictable.core.elements)
+    init(periodictable.core.default_table())
 
 This would be fine for the current example because the table size is
 small and load time is fast.  For large tables, you may wish to

periodictable/fasta.py

@@ -544,11 +544,26 @@ def fasta_table():
 
 beta_casein = "RELEELNVPGEIVESLSSSEESITRINKKIEKFQSEEQQQTEDELQDKIHPFAQTQSLVYPFPGPIPNSLPQNIPPLTQTPVVVPPFLQPEVMGVSKVKEAMAPKHKEMPFPKYPVEPFTESQSLTLTDVENLHLPLPLLQSWMHQPHQPLPPTVMFPPQSVLSLSQSKVLPVPQKAVPYPQRDMPIQAFLLYQEPVLGPVRGPFPIIV"
 
+## Uncomment to show package path on CI infrastructure
+#def doctestpath():
+#    """
+#    Checking import path for doctests::
+#
+#        >>> import periodictable
+#        >>> print(f"Path to imported periodictable in docstr is {periodictable.__file__}")
+#        some path printed here
+#    """
+
 def test():
     from periodictable.constants import avogadro_number
     from .formulas import formula
     elements = default_table()
 
+    ## Uncomment to show package path on CI infrastructure
+    #import periodictable
+    #print(f"Path to imported periodictable in package is {periodictable.__file__}")
+    #print(fail_test)
+
     # Beta casein results checked against Duncan McGillivray's spreadsheet
     # name        Hmass   Dmass   vol     den   #el   xray  Hsld  Dsld
     # =========== ======= ======= ======= ===== ===== ===== ===== =====

pyproject.toml

@@ -11,13 +11,14 @@ dependencies = [
     "pyparsing", "numpy",
 ]
 
-[project.optional-dependencies]
-dev = [
-    'build',
-    'pytest',
-    'pytest-cov',
-    'sphinx',
-]
+#[project.optional-dependencies]
+#dev = [
+#    "build",
+#    "pytest",
+#    "pytest-cov",
+#    "matplotlib",
+#    "sphinx",
+#]
 
 classifiers=[
     "Development Status :: 5 - Production/Stable",
@@ -49,7 +50,8 @@ packages = ["periodictable"]
 [tool.pytest.ini_options]
 addopts = ["--doctest-modules", "--doctest-glob=*.rst", "--cov=periodictable"]
 doctest_optionflags = "ELLIPSIS"
+pythonpath = ["doc/sphinx"]
 testpaths = ["periodictable", "test", "doc/sphinx/guide"]
 python_files = "*.py"
 python_classes = "NoClassTestsWillMatch"
-python_functions = ["test", "*_test", "test_*", "model_tests"]
+python_functions = ["test", "*_test", "test_*"]

test/test_core.py

@@ -1,6 +1,10 @@
 from periodictable import H, O, Fe, helium, elements, data_files
 
 def test():
+    ## Uncomment to print the package path on the CI infrastructure
+    #import periodictable
+    #print(f"Path to imported periodictable in test dir is {periodictable.__file__}")
+    #print(fail_test)
     # Check that we can access element properties
     assert H.name == "hydrogen"
     assert H.symbol == "H"