ICAMS · yury-lysogorskiy · Nov 23, 2021 · Nov 22, 2021 · Nov 22, 2021 · Nov 22, 2021
diff --git a/.github/publish-to-test-pypi.yml b/.github/publish-to-test-pypi.yml
@@ -0,0 +1,36 @@
+name: Publish to TestPyPI
+on: push
+jobs:
+  build-n-publish:
+    name: Build and publish Python distributions to TestPyPI
+    runs-on: ubuntu-18.04
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+    - name: Publish distribution to Test PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+    # - name: Publish distribution 📦 to PyPI
+    #   if: startsWith(github.ref, 'refs/tags')
+    #   uses: pypa/gh-action-pypi-publish@master
+    #   with:
+    #     password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/doc/build_doc.sh → docs/build_doc.sh b/doc/build_doc.sh → docs/build_doc.sh
diff --git a/docs/make.bat b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/doc/pacemaker.html → docs/pacemaker.html b/doc/pacemaker.html → docs/pacemaker.html
diff --git a/doc/pacemaker.pdf → docs/pacemaker.pdf b/doc/pacemaker.pdf → docs/pacemaker.pdf
diff --git a/doc/pandoc.css → docs/pandoc.css b/doc/pandoc.css → docs/pandoc.css
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,6 @@
+sphinx
+sphinx_rtd_theme
+m2r2
+sphinx-rtd-theme
+sphinx-markdown-tables
+cmake
diff --git a/docs/source/_static/.gitkeep b/docs/source/_static/.gitkeep
diff --git a/docs/source/_templates/.gitkeep b/docs/source/_templates/.gitkeep
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,86 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+import shutil
+import glob
+
+#add system path
+sys.path.insert(0, os.path.abspath('../../pyace/'))
+
+#now these lines can be commented back in to read in images
+#cdir = os.getcwd()
+#figs = glob.glob("../../examples/*/*.png")
+#for fig in figs:
+#    shutil.copy(fig, "../_static/")
+
+
+#required for skipping
+def skip(app, what, name, obj, would_skip, options):
+    if name in ( '__init__',):
+        return False
+    return would_skip
+def setup(app):
+    app.connect('autodoc-skip-member', skip)
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'python-ace'
+copyright = '2021, Yury Lysogorskiy, Anton Bochkarev, Sarath Menon, Ralf Drautz'
+author = 'Yury Lysogorskiy, Anton Bochkarev, Sarath Menon, Ralf Drautz'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+    'm2r2',
+    'sphinx_markdown_tables',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+html_theme_options = {
+    "sidebar_hide_name": True,
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_extra_path = ['../_static' ]
+#html_static_path = ['_static']
+#
+source_suffix = ['.rst', '.md']
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,37 @@
+.. python-ace documentation master file, created by
+   sphinx-quickstart on Mon Nov 22 13:23:23 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+pacemaker
+=========
+
+`pacemaker` is a tool for fitting of interatomic potentials in a general nonlinear Atomic Cluster Expansion (ACE) form.
+
+
+Documentation
+~~~~~~~~~~~~~
+
+.. toctree::
+   pacemaker/install
+   pacemaker/quickstart
+   pacemaker/workflow
+   pacemaker/inputfile
+   pacemaker/cli
+   pacemaker/utilities
+   pacemaker/faq
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
@@ -0,0 +1,7 @@
+pyace
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   pyace
diff --git a/doc/pacemaker.md → docs/source/pacemaker.md b/doc/pacemaker.md → docs/source/pacemaker.md
diff --git a/doc/Scheme_ext.png → docs/source/pacemaker/Scheme_ext.png b/doc/Scheme_ext.png → docs/source/pacemaker/Scheme_ext.png
diff --git a/docs/source/pacemaker/cli.md b/docs/source/pacemaker/cli.md
@@ -0,0 +1,46 @@
+# `pacemaker` command line interface
+
+`pacemaker` is an utility for fitting the atomic cluster expansion potential. Usage:
+
+```
+usage: pacemaker [-h] [-c] [-o OUTPUT] [-p POTENTIAL] [-ip INITIAL_POTENTIAL]
+                 [-b BACKEND] [-d DATA] [--query-data] [--prepare-data]
+                 [--rebuild] [-l LOG] [-dr] [-t]
+                 [input]
+
+Fitting utility for atomic cluster expansion potentials
+
+positional arguments:
+  input                 input YAML file, default: input.yaml
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c, --clean           Remove all generated data
+  -o OUTPUT, --output OUTPUT
+                        output B-basis YAML file name, default:
+                        output_potential.yaml
+  -p POTENTIAL, --potential POTENTIAL
+                        input potential YAML file name, will override input
+                        file 'potential' section
+  -ip INITIAL_POTENTIAL, --initial-potential INITIAL_POTENTIAL
+                        initial potential YAML file name, will override input
+                        file 'potential::initial_potential' section
+  -b BACKEND, --backend BACKEND
+                        backend evaluator, will override section
+                        'backend::evaluator' from input file
+  -d DATA, --data DATA  data file, will override section 'YAML:fit:filename'
+                        from input file
+  --query-data          query the training data from database, prepare and
+                        save them
+  --prepare-data        prepare and save training data only
+  --rebuild             force to rebuild necessary neighbour lists
+  -l LOG, --log LOG     log filename, default: log.txt
+  -dr, --dry-run        Dry run: performs all preprocessing and analysis, but
+                        do not do the fitting
+  -t, --template        Create a template 'input.yaml' file
+  -v, --version         Show version info
+  --no-fit              Do not fit the potential
+  --no-predict          Do not compute and save the predictions
+  --verbose-tf          Make tensorflow more verbose (off by defeault)
+
+```