Replace unused 'non-extra' reqs that conflicted with extras with the …

…full set of reqs

.github/workflows/release.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Install dependencies
         run: |
           python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools build setuptools setuptools_scm wheel
-          python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}.txt
           # Using non-editable install for testing building of MANIFEST files
           python${{ matrix.python-version }} -m pip install --no-deps .
 

.github/workflows/test.yml

@@ -56,7 +56,7 @@ jobs:
     - name: Install Python dependencies
       run: |
         python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools setuptools setuptools_scm
-        python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+        python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}.txt
         # Using non-editable install for testing building of MANIFEST files
         python${{ matrix.python-version }} -m pip install --no-deps .
         python${{ matrix.python-version }} -m pip install pre-commit

.github/workflows/upgrade-dependencies.yml

@@ -28,8 +28,7 @@ jobs:
         shell: bash
         run: |
           python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools
-          python${{ matrix.python-version }} -m piptools compile -q --upgrade -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}.txt
-          python${{ matrix.python-version }} -m piptools compile -q --upgrade --all-extras -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
+          python${{ matrix.python-version }} -m piptools compile -q --upgrade --all-extras -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}.txt
       - name: Detect changes
         id: changes
         shell: bash

requirements/macos-latest_py3.10.txt

@@ -2,38 +2,133 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile --output-file=requirements/macos-latest_py3.10.txt
+#    pip-compile --all-extras --output-file=requirements/macos-latest_py3.10_extras.txt
 #
+aflow==0.0.11
+    # via matminer (setup.py)
+alabaster==0.7.13
+    # via sphinx
+ase==3.22.1
+    # via
+    #   aflow
+    #   dscribe
+    #   matminer (setup.py)
+astroid==2.15.6
+    # via pylint
+attrs==23.1.0
+    # via
+    #   jsonschema
+    #   referencing
+babel==2.12.1
+    # via sphinx
+beautifulsoup4==4.12.2
+    # via aflow
+black==23.7.0
+    # via matminer (setup.py)
 certifi==2023.7.22
     # via requests
+cffi==1.15.1
+    # via cryptography
 charset-normalizer==3.2.0
     # via requests
+citrination-client==6.5.1
+    # via matminer (setup.py)
+click==8.1.7
+    # via black
 contourpy==1.1.0
     # via matplotlib
+coverage[toml]==6.5.0
+    # via
+    #   coveralls
+    #   matminer (setup.py)
+    #   pytest-cov
+coveralls==3.3.1
+    # via matminer (setup.py)
+cryptography==41.0.3
+    # via
+    #   globus-sdk
+    #   pyjwt
 cycler==0.11.0
     # via matplotlib
+dill==0.3.7
+    # via pylint
 dnspython==2.4.2
     # via pymongo
+docopt==0.6.2
+    # via coveralls
+docutils==0.20.1
+    # via sphinx
+dscribe==2.1.0
+    # via matminer (setup.py)
 emmet-core==0.67.5
     # via mp-api
+exceptiongroup==1.1.3
+    # via pytest
+fair-research-login==0.3.1
+    # via mdf-toolbox
+flake8==6.1.0
+    # via matminer (setup.py)
 fonttools==4.42.1
     # via matplotlib
 future==0.18.3
     # via
     #   matminer (setup.py)
     #   uncertainties
+globus-nexus-client==0.4.1
+    # via mdf-toolbox
+globus-sdk==3.28.0
+    # via
+    #   fair-research-login
+    #   globus-nexus-client
+    #   mdf-forge
+    #   mdf-toolbox
+httplib2==0.22.0
+    # via matminer (setup.py)
 idna==3.4
     # via requests
+imagesize==1.4.1
+    # via sphinx
+iniconfig==2.0.0
+    # via pytest
+isort==5.12.0
+    # via pylint
+jinja2==3.1.2
+    # via
+    #   aflow
+    #   sphinx
+jmespath==1.0.1
+    # via matminer (setup.py)
 joblib==1.3.2
     # via
+    #   dscribe
     #   pymatgen
     #   scikit-learn
+jsonschema==4.3.0
+    # via
+    #   matminer (setup.py)
+    #   mdf-toolbox
 kiwisolver==1.4.5
     # via matplotlib
 latexcodec==2.0.1
     # via pybtex
+lazy-object-proxy==1.9.0
+    # via astroid
+llvmlite==0.40.1
+    # via numba
+markupsafe==2.1.3
+    # via jinja2
 matplotlib==3.7.2
-    # via pymatgen
+    # via
+    #   ase
+    #   pymatgen
+mccabe==0.7.0
+    # via
+    #   flake8
+    #   pylint
+mdf-forge==0.8.0
+    # via matminer (setup.py)
+mdf-toolbox==0.6.0
+    # via mdf-forge
 monty==2023.9.5
     # via
     #   emmet-core
@@ -46,40 +141,75 @@ mpmath==1.3.0
     # via sympy
 msgpack==1.0.5
     # via mp-api
+mypy-extensions==1.0.0
+    # via black
 networkx==3.1
     # via pymatgen
-numpy==1.25.2
+numba==0.57.1
+    # via sparse
+numpy==1.24.4
     # via
+    #   aflow
+    #   ase
     #   contourpy
+    #   dscribe
     #   matminer (setup.py)
     #   matplotlib
+    #   numba
     #   pandas
     #   pymatgen
+    #   pypif
     #   scikit-learn
     #   scipy
+    #   sparse
     #   spglib
 packaging==23.1
     # via
+    #   black
     #   matplotlib
     #   plotly
+    #   pytest
+    #   sphinx
 palettable==3.3.3
     # via pymatgen
 pandas==2.1.0
     # via
     #   matminer (setup.py)
     #   pymatgen
+pathspec==0.11.2
+    # via black
 pillow==10.0.0
     # via matplotlib
+platformdirs==3.10.0
+    # via
+    #   black
+    #   pylint
 plotly==5.16.1
     # via pymatgen
+pluggy==1.3.0
+    # via pytest
+pybind11==2.11.1
+    # via dscribe
 pybtex==0.24.0
     # via
     #   emmet-core
     #   pymatgen
+pycodestyle==2.11.0
+    # via flake8
+pycparser==2.21
+    # via cffi
 pydantic==1.10.12
     # via
     #   emmet-core
     #   pymatgen
+pyflakes==3.1.0
+    # via flake8
+pygments==2.16.1
+    # via sphinx
+pyjwt[crypto]==2.8.0
+    # via globus-sdk
+pylint==2.17.5
+    # via matminer (setup.py)
 pymatgen==2023.9.2
     # via
     #   emmet-core
@@ -88,39 +218,96 @@ pymatgen==2023.9.2
 pymongo==4.5.0
     # via matminer (setup.py)
 pyparsing==3.0.9
-    # via matplotlib
+    # via
+    #   httplib2
+    #   matplotlib
+pypif==2.1.2
+    # via citrination-client
+pyrsistent==0.19.3
+    # via jsonschema
+pytest==7.4.1
+    # via
+    #   matminer (setup.py)
+    #   pytest-cov
+    #   pytest-timeout
+pytest-cov==4.1.0
+    # via matminer (setup.py)
+pytest-timeout==2.1.0
+    # via matminer (setup.py)
 python-dateutil==2.8.2
     # via
     #   matplotlib
     #   pandas
 pytz==2023.3.post1
     # via pandas
 pyyaml==6.0.1
-    # via pybtex
+    # via
+    #   citrination-client
+    #   pybtex
 requests==2.31.0
     # via
+    #   citrination-client
+    #   coveralls
+    #   globus-sdk
     #   matminer (setup.py)
+    #   mdf-forge
+    #   mdf-toolbox
     #   mp-api
     #   pymatgen
+    #   sphinx
 ruamel-yaml==0.17.32
     # via pymatgen
 ruamel-yaml-clib==0.2.7
     # via ruamel-yaml
 scikit-learn==1.3.0
-    # via matminer (setup.py)
+    # via
+    #   dscribe
+    #   matminer (setup.py)
 scipy==1.11.2
     # via
+    #   ase
+    #   dscribe
     #   pymatgen
     #   scikit-learn
+    #   sparse
 six==1.16.0
     # via
+    #   aflow
+    #   citrination-client
     #   latexcodec
     #   pybtex
+    #   pypif
     #   python-dateutil
+snowballstemmer==2.2.0
+    # via sphinx
+soupsieve==2.5
+    # via beautifulsoup4
+sparse==0.14.0
+    # via dscribe
 spglib==2.0.2
     # via
     #   emmet-core
     #   pymatgen
+sphinx==7.2.5
+    # via
+    #   matminer (setup.py)
+    #   sphinxcontrib-applehelp
+    #   sphinxcontrib-devhelp
+    #   sphinxcontrib-htmlhelp
+    #   sphinxcontrib-qthelp
+    #   sphinxcontrib-serializinghtml
+sphinxcontrib-applehelp==1.0.7
+    # via sphinx
+sphinxcontrib-devhelp==1.0.5
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.4
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.6
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.9
+    # via sphinx
 sympy==1.12
     # via
     #   matminer (setup.py)
@@ -129,23 +316,39 @@ tabulate==0.9.0
     # via pymatgen
 tenacity==8.2.3
     # via plotly
+termcolor==2.3.0
+    # via aflow
 threadpoolctl==3.2.0
     # via scikit-learn
+tomli==2.0.1
+    # via
+    #   black
+    #   coverage
+    #   pylint
+    #   pytest
+tomlkit==0.12.1
+    # via pylint
 tqdm==4.66.1
     # via
     #   matminer (setup.py)
+    #   mdf-forge
     #   pymatgen
 typing-extensions==4.7.1
     # via
+    #   astroid
     #   emmet-core
     #   mp-api
     #   pydantic
 tzdata==2023.3
     # via pandas
+ujson==5.8.0
+    # via matminer (setup.py)
 uncertainties==3.1.7
     # via pymatgen
 urllib3==2.0.4
     # via requests
+wrapt==1.15.0
+    # via astroid
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools