Support exit code (#3)

1) modify the `exectue` method, so that it does not raise if the calculation failed, so that we can parse the result and return an exit_code
2) use the parser from aiida-quantumespresso to parse the results
3) add docs
4) add tests

.github/workflows/ci.yaml

@@ -0,0 +1,71 @@
+name: ci
+
+on: [push, pull_request]
+
+jobs:
+
+    pre-commit:
+
+        runs-on: ubuntu-latest
+
+        steps:
+        -   uses: actions/checkout@v2
+
+        -   name: Cache Python dependencies
+            uses: actions/cache@v1
+            with:
+                path: ~/.cache/pip
+                key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+                restore-keys:
+                    pip-pre-commit-
+
+        -   name: Set up Python
+            uses: actions/setup-python@v2
+            with:
+                python-version: '3.10'
+
+        -   name: Install Python dependencies
+            run: pip install -e .[pre-commit,tests]
+
+        -   name: Run pre-commit
+            run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+    test:
+
+        runs-on: ubuntu-latest
+
+        strategy:
+            matrix:
+                python-version: ['3.11']
+
+        steps:
+        -   uses: actions/checkout@v2
+
+        -   name: Cache Python dependencies
+            uses: actions/cache@v1
+            with:
+                path: ~/.cache/pip
+                key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+                restore-keys:
+                    pip-${{ matrix.python-version }}-tests
+
+        -   name: Set up Python ${{ matrix.python-version }}
+            uses: actions/setup-python@v2
+            with:
+                python-version: ${{ matrix.python-version }}
+
+        -   name: Install system dependencies
+            run: sudo apt update && sudo apt install --no-install-recommends libfftw3-dev quantum-espresso
+
+        -   name: Install Python dependencies
+            run: |
+                pip install -e .[pre-commit,tests]
+
+        -   name: Run pytest
+            run: |
+                pytest -v tests --cov
+        -   name: Upload coverage reports to Codecov
+            uses: codecov/codecov-action@v4.0.1
+            with:
+                token: ${{ secrets.CODECOV_TOKEN }}
+                flags: python-${{ matrix.python-version }}

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+# Build from the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: docs/requirements.txt

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)

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
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx_rtd_theme==1.2.2
+nbsphinx==0.9.2
+ipython

docs/source/conf.py

@@ -0,0 +1,91 @@
+# 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
+from pathlib import Path
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "ASE QuantumESPRESSO"
+copyright = "2024, Xing Wang"
+author = "Xing Wang"
+
+# The full version, including alpha/beta/rc tags
+release = "0.0.1"
+
+
+# -- 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_rtd_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "nbsphinx",
+]
+
+# 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 = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# 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_static_path = ["_static"]
+
+
+# Function to copy HTML files
+def copy_html_files(app, exception):
+    """
+    Copy all .html files from source to build directory, maintaining the directory structure.
+    """
+    print("Copying HTML files to build directory")
+    if exception is not None:  # Only copy files if the build succeeded
+        print(
+            "Build failed, but we still try to copy the HTML files to the build directory"
+        )
+    try:
+        src_path = Path(app.builder.srcdir)
+        build_path = Path(app.builder.outdir)
+        for html_file in src_path.rglob("*.html"):
+            relative_path = html_file.relative_to(src_path)
+            destination_file = build_path / relative_path
+            destination_file.parent.mkdir(parents=True, exist_ok=True)
+            shutil.copy(html_file, destination_file)
+    except Exception as e:
+        print(f"Failed to copy HTML files: {e}")
+
+
+def setup(app):
+    app.connect("build-finished", copy_html_files)

docs/source/howtos/index.rst

@@ -0,0 +1,13 @@
+Quantum ESPRESSO
+===========================================
+
+Here are the collection of WorkGraphs for Quantum ESPRESSO
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   base
+   pw
+   dos
+   projwfc

docs/source/index.rst

@@ -0,0 +1,23 @@
+
+Welcome to WorkGraph Collections' documentation!
+===================================================
+
+Extends the functionality of ASE espresso module by providing additional calculators for Quantum ESPRESSO binaries, including pw.x, dos.x, pp.x, and others.
+
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   installation
+   quickstart
+   howtos/index
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/installation.rst

@@ -0,0 +1,16 @@
+============
+Installation
+============
+
+
+The recommended method of installation is to use the Python package manager |pip|_:
+
+.. code-block:: console
+
+    $ pip install ase-quantumespresso
+
+
+This will install the latest version.
+
+
+.. _pip: https://pip.pypa.io/en/stable/