Merge pull request #35 from wolearyc/dev

0.5.0
wolearyc · Oct 3, 2024 · 8404456 · 8404456
2 parents 89355f3 + fb26028
commit 8404456
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -9,11 +9,12 @@ updates:
     directory: "/"
     schedule:
       interval: weekly
-    target-branch: "dev"
     groups:
       python-packages:
         patterns:
           - "*"
+        exclude-patterns:
+          - "*torch*"
 
   - package-ecosystem: github-actions
     directory: "/"

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -29,6 +29,7 @@ jobs:
         pip install uv
         uv pip install ${{ matrix.uv-arg }} --system -r deps/dev_requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system -r deps/requirements.txt
+        uv pip install ${{ matrix.uv-arg }} --system -r deps/pymatgen_requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system -r deps/torch_geometric_requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system -r deps/torch_requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system --no-index -r deps/torch_extra_requirements.txt

diff --git a/.gitignore b/.gitignore
@@ -269,3 +269,4 @@ test/data/temp
 test/data/temp.vasp
 docs/source/notebooks/*POSCAR
 test/Testing.ipynb
+test/data/scratch/*
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,6 +9,7 @@ python:
   install:
     - requirements: docs/requirements.txt
     - requirements: deps/requirements.txt
+    - requirements: deps/pymatgen_requirements.txt
     - requirements: deps/torch_requirements.txt
     - requirements: deps/torch_geometric_requirements.txt
     - requirements: deps/torch_extra_requirements.txt

diff --git a/README.md b/README.md
@@ -45,7 +45,13 @@ $ pip install torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.4.0
 $ pip install ramannoodle[torch]
 ```
 
-## Documentation
+Ramannoodle includes interfaces with [pymatgen](https://pymatgen.org/). To use these interfaces, ramannoodle should be installed with the `pymatgen` options group:
+
+```
+$ pip install ramannoodle[pymatgen]
+```
+
+## Tutorials and docs
 
 [https://ramannoodle.readthedocs.io/](https://ramannoodle.readthedocs.io/)
 

diff --git a/deps/pymatgen_requirements.txt b/deps/pymatgen_requirements.txt
@@ -0,0 +1,17 @@
+matplotlib >= 3.7.0 # min recommended
+mpmath >= 1.2.0
+pandas >= 2.0.0 # min recommended
+pillow >= 8.3.2;python_version=='3.10' and sys_platform=='darwin'  # working
+pillow >= 8.3.2;python_version=='3.10' and sys_platform=='win32'   # working
+pillow >= 8.3.2;python_version=='3.10' and sys_platform=='linux'   # min recommended
+pillow >= 8.3.2;python_version=='3.11' and sys_platform=='darwin'  # min recommended
+pillow >= 10.0.0;python_version=='3.11' and sys_platform=='win32'  # working
+pillow >= 8.3.2;python_version=='3.11' and sys_platform=='linux'   # min recommended
+pillow >= 10.1.0;python_version=='3.12' and sys_platform=='darwin'  # working
+pillow >= 10.1.0;python_version=='3.12' and sys_platform=='win32'  # working
+pillow >= 10.1.0;python_version=='3.12' and sys_platform=='linux'   # min recommended
+pymatgen >= 2024.8.9 # min working
+pyparsing >= 3.0.0 # min working
+ruamel-yaml >= 0.17.2
+sympy >= 1.13.3;python_version=='3.12'
+uncertainties >= 3.1.7
diff --git a/docs/coverage-badge.svg b/docs/coverage-badge.svg
diff --git a/docs/gen_api_sources.sh b/docs/gen_api_sources.sh
@@ -1,2 +1,2 @@
-# CD must be the reports directory!
-sphinx-apidoc -o source/generated ../ramannoodle
+# CD must be the docs directory
+sphinx-apidoc --module-first --remove-old -f --templatedir=source/_templates -f  --remove-old -o source/generated ../ramannoodle
diff --git a/docs/gen_test_coverage_badges.sh b/docs/gen_test_coverage_badges.sh
@@ -1,4 +1,4 @@
-# CD must be the reports directory!
+# CD must be the docs directory!
 cd ..
 coverage run -m pytest --junitxml=reports/junit/junit.xml test
 coverage xml -o  reports/coverage/coverage.xml

diff --git a/docs/source/_templates/module.rst.jinja b/docs/source/_templates/module.rst.jinja
@@ -0,0 +1,8 @@
+{%- if show_headings %}
+{{- [basename, "module"] | join(' ') | e | heading }}
+
+{% endif -%}
+.. automodule:: {{ qualname }}
+{%- for option in automodule_options %}
+   :{{ option }}:
+{%- endfor %}
diff --git a/docs/source/_templates/package.rst.jinja b/docs/source/_templates/package.rst.jinja
@@ -0,0 +1,57 @@
+{%- macro automodule(modname, options) -%}
+.. automodule:: {{ modname }}
+{%- for option in options %}
+   :{{ option }}:
+{%- endfor %}
+{%- endmacro %}
+
+{%- macro toctree(docnames) -%}
+.. toctree::
+   :maxdepth: {{ maxdepth }}
+{% for docname in docnames %}
+   {{ docname }}
+{%- endfor %}
+{%- endmacro %}
+
+{%- if is_namespace %}
+{{- [pkgname, ""] | join(" ") | e | heading }}
+{% else %}
+{{- [pkgname, ""] | join(" ") | e | heading }}
+{% endif %}
+
+{%- if is_namespace %}
+.. py:module:: {{ pkgname }}
+{% endif %}
+
+{%- if modulefirst and not is_namespace %}
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}
+
+{%- if subpackages %}
+Subpackages
+-----------
+
+{{ toctree(subpackages) }}
+{% endif %}
+
+{%- if submodules %}
+Submodules
+----------
+{% if separatemodules %}
+{{ toctree(submodules) }}
+{% else %}
+{%- for submodule in submodules %}
+{% if show_headings %}
+{{- [submodule, "module"] | join(" ") | e | heading(2) }}
+{% endif %}
+{{ automodule(submodule, automodule_options) }}
+{% endfor %}
+{%- endif %}
+{%- endif %}
+
+{%- if not modulefirst and not is_namespace %}
+Module contents
+---------------
+
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -38,6 +38,7 @@
     'numpy': ('http://docs.scipy.org/doc/numpy', None),
     'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
     'torch': ('https://pytorch.org/docs/stable/', None),
+    'pymatgen': ('https://pymatgen.org', None),
 }
 
 intersphinx_disabled_domains = ['std']
@@ -51,6 +52,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'furo'
+html_title = 'ramannoodle'
 html_static_path = ['_static']
 html_theme_options = {
     "light_logo": "logo.png",

diff --git a/docs/source/generated/ramannoodle.dataset.rst b/docs/source/generated/ramannoodle.dataset.rst
@@ -1,5 +1,10 @@
-ramannoodle.dataset package
-===========================
+ramannoodle.dataset
+====================
+
+.. automodule:: ramannoodle.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Subpackages
 -----------
@@ -8,11 +13,3 @@ Subpackages
    :maxdepth: 4
 
    ramannoodle.dataset.torch
-
-Module contents
----------------
-
-.. automodule:: ramannoodle.dataset
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/ramannoodle.dataset.torch.rst b/docs/source/generated/ramannoodle.dataset.torch.rst
@@ -1,29 +1,18 @@
-ramannoodle.dataset.torch package
-=================================
+ramannoodle.dataset.torch
+==========================
 
-Submodules
-----------
-
-ramannoodle.dataset.torch.dataset module
-----------------------------------------
-
-.. automodule:: ramannoodle.dataset.torch.dataset
+.. automodule:: ramannoodle.dataset.torch
    :members:
    :undoc-members:
    :show-inheritance:
 
+Submodules
+----------
+
 ramannoodle.dataset.torch.utils module
 --------------------------------------
 
 .. automodule:: ramannoodle.dataset.torch.utils
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: ramannoodle.dataset.torch
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/ramannoodle.dynamics.rst b/docs/source/generated/ramannoodle.dynamics.rst
@@ -1,27 +1,5 @@
-ramannoodle.dynamics package
-============================
-
-Submodules
-----------
-
-ramannoodle.dynamics.phonon module
-----------------------------------
-
-.. automodule:: ramannoodle.dynamics.phonon
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-ramannoodle.dynamics.trajectory module
---------------------------------------
-
-.. automodule:: ramannoodle.dynamics.trajectory
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
+ramannoodle.dynamics
+=====================
 
 .. automodule:: ramannoodle.dynamics
    :members:

diff --git a/docs/source/generated/ramannoodle.io.rst b/docs/source/generated/ramannoodle.io.rst
@@ -1,5 +1,10 @@
-ramannoodle.io package
-======================
+ramannoodle.io
+===============
+
+.. automodule:: ramannoodle.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Subpackages
 -----------
@@ -20,18 +25,10 @@ ramannoodle.io.generic module
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.io.utils module
----------------------------
+ramannoodle.io.pymatgen module
+------------------------------
 
-.. automodule:: ramannoodle.io.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: ramannoodle.io
+.. automodule:: ramannoodle.io.pymatgen
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/source/generated/ramannoodle.io.vasp.rst b/docs/source/generated/ramannoodle.io.vasp.rst
@@ -1,5 +1,10 @@
-ramannoodle.io.vasp package
-===========================
+ramannoodle.io.vasp
+====================
+
+.. automodule:: ramannoodle.io.vasp
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Submodules
 ----------
@@ -35,11 +40,3 @@ ramannoodle.io.vasp.xdatcar module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: ramannoodle.io.vasp
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/ramannoodle.pmodel.rst b/docs/source/generated/ramannoodle.pmodel.rst
@@ -1,5 +1,10 @@
-ramannoodle.pmodel package
-==========================
+ramannoodle.pmodel
+===================
+
+.. automodule:: ramannoodle.pmodel
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Subpackages
 -----------
@@ -8,30 +13,3 @@ Subpackages
    :maxdepth: 4
 
    ramannoodle.pmodel.torch
-
-Submodules
-----------
-
-ramannoodle.pmodel.art module
------------------------------
-
-.. automodule:: ramannoodle.pmodel.art
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-ramannoodle.pmodel.interpolation module
----------------------------------------
-
-.. automodule:: ramannoodle.pmodel.interpolation
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: ramannoodle.pmodel
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/ramannoodle.pmodel.torch.rst b/docs/source/generated/ramannoodle.pmodel.torch.rst
@@ -1,35 +1,5 @@
-ramannoodle.pmodel.torch package
-================================
-
-Submodules
-----------
-
-ramannoodle.pmodel.torch.gnn module
------------------------------------
-
-.. automodule:: ramannoodle.pmodel.torch.gnn
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-ramannoodle.pmodel.torch.train module
--------------------------------------
-
-.. automodule:: ramannoodle.pmodel.torch.train
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-ramannoodle.pmodel.torch.utils module
--------------------------------------
-
-.. automodule:: ramannoodle.pmodel.torch.utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
+ramannoodle.pmodel.torch
+=========================
 
 .. automodule:: ramannoodle.pmodel.torch
    :members: