chore: merge main into branch to resolve merge conflict

.gitignore

@@ -0,0 +1,162 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

Dockerfile

@@ -1,3 +1,4 @@
+# Docker image used for performing installation tests with GitHub Actions
 FROM python:3.12
 
 # Install system dependencies

README.md

@@ -1,8 +1,8 @@
 # py2spack: Automating conversion of standard python packages to Spack package recipes
 
-Github repository for the CSCS internship project with the goal of developing a Python tool for automatically generating Spark package recipes based on existing Python packages, with the ability to handle direct and transitive dependencies and flexible versions.
+Github repository for the CSCS internship project with the goal of developing a Python tool for automatically generating Spack package recipes based on existing Python packages, with the ability to handle direct and transitive dependencies and flexible versions.
 
-For more information, see the [Wiki](https://github.com/davhofer/py2spack/wiki).
+For more information, see the [Documentation](#Documentation).
 
 ## Installation
 
@@ -33,10 +33,7 @@ The package is still in development and not yet published to PyPI. It can howeve
 ## Usage
 
 ```
-usage: py2spack [-h] [--max-conversions MAX_CONVERSIONS]
-                [--versions-per-package VERSIONS_PER_PACKAGE]
-                [--repo REPO] [--ignore [IGNORE ...]] [--testing]
-                package
+usage: py2spack [-h] [--max-conversions MAX_CONVERSIONS] [--versions-per-package VERSIONS_PER_PACKAGE] [--repo REPO] [--allow-duplicate] package [--ignore [IGNORE ...]]
 
 CLI for converting a python package and its dependencies to Spack.
 
@@ -48,16 +45,11 @@ options:
   --max-conversions MAX_CONVERSIONS
                         Maximum number of packages that are converted
   --versions-per-package VERSIONS_PER_PACKAGE
-                        Versions per package to be downloaded and
-                        converted
-  --repo REPO           Name of or full path to local Spack
-                        repository where packages should be saved
+                        Versions per package to be downloaded and converted
+  --repo REPO           Name of or full path to local Spack repository where packages should be saved
   --ignore [IGNORE ...]
-                        List of packages to ignore. Must be specified
-                        last (after <package> argument) for the
-                        command to work
-  --testing             For testing purposes; adds the prefix 'test-'
-                        when saving packages
+                        List of packages to ignore. Must be specified last (after <package> argument) for the command to work
+  --allow-duplicate     Convert the package, even if a package of the same name already exists in some Spack repo. Will NOT overwrite the existing package. Only applies to the main package to be converted, not to dependencies.
 ```
 
 ### Conversion from PyPI
@@ -80,16 +72,31 @@ py2spack user/package-name
 
 > NOTE: dependencies will always be resolved through PyPI, even when converting a package from GitHub
 
-## Running tests
+## Documentation
 
-After installing the package, the tests can be run from the project root directory as follows:
+To check out the detailed documentation (API docs, usage, implementation, package conversion, etc.), you need to clone the repository and build the docs:
+
+```bash
+pip install .[docs]
+cd docs; make html
+```
+
+You can then browse it locally, e.g.
+
+```bash
+firefox _build/html/index.html
+```
+
+## Testing
+
+After installing the package with the `tests` option, the tests can be run from the project root directory as follows:
 
 ```bash
 python -m pytest
 ```
 
-## Important links
+Installation tests for converted packages are run through GitHub Actions in a Docker container, see `.github/workflows/run-installation-tests.yaml`.
+
+## Author
 
-- [Detailed Project Description](<CSCS Internship Project Description.md>)
-- [Wiki](https://github.com/davhofer/py2spack/wiki)
-- [Changelog](CHANGELOG.md)
+Created by David Hofer ([davhofer](https://github.com/davhofer), `davhofer [at] ethz [dot] ch`) during an internship at [CSCS](https://www.cscs.ch/).

docs/.gitignore

@@ -0,0 +1,2 @@
+_build/
+apidocs/

docs/Makefile

@@ -0,0 +1,27 @@
+# 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     = .
+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) $(O)
+
+# raise warnings to errors
+html-strict:
+	@$(SPHINXBUILD) -b html -nW --keep-going "$(SOURCEDIR)" "$(BUILDDIR)/html" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -r $(BUILDDIR)