updated doc

kunwuz · kunwuz · commit 7df990d11044 · 2023-08-01T02:54:49.000-04:00
diff --git a/README.md b/README.md
@@ -70,3 +70,16 @@ We are always targeting to make our community better!
 # Running Tetrad in Python
 
 Although causal-learn provides python implementations for some causal discovery algorithms, there are currently a lot more in the classical Java-based [Tetrad](https://github.com/cmu-phil/tetrad) program. For users who would like to incorporate arbitrary Java code in Tetrad as part of a Python workflow, we strongly recommend considering [py-tetrad](https://github.com/cmu-phil/py-tetrad). Here is a list of [reusable examples](https://github.com/cmu-phil/py-tetrad/tree/main/pytetrad) of how to painlessly benefit from the most comprehensive Tetrad Java codebase.
+
+# Citation
+
+Please cite as:
+
+```
+@article{causallearn,
+  title={Causal-learn: Causal Discovery in Python},
+  author={Yujia Zheng and Biwei Huang and Wei Chen and Joseph Ramsey and Mingming Gong and Ruichu Cai and Shohei Shimizu and Peter Spirtes and Kun Zhang},
+  journal={arXiv preprint arXiv:2307.16405},
+  year={2023}
+}
+```
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1,211 @@
+.idea/*
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Python template
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -81,5 +81,18 @@ Contributors
 
 **Quality control**: Yewen Fan, Haoyue Dai, Yujia Zheng, Ignavier Ng, Xiangchen Song
 
+Citation
+^^^^^^^^^^^^
+
+Please cite as:
+
+  @article{causallearn,
+    title={Causal-learn: Causal Discovery in Python},
+    author={Yujia Zheng and Biwei Huang and Wei Chen and Joseph Ramsey and Mingming Gong and Ruichu Cai and Shohei Shimizu and Peter Spirtes and Kun Zhang},
+    journal={arXiv preprint arXiv:2307.16405},
+    year={2023}
+  }
+
+
 
 
diff --git a/docs/source/search_methods_index/Constraint-based causal discovery methods/FCI.rst b/docs/source/search_methods_index/Constraint-based causal discovery methods/FCI.rst
@@ -56,6 +56,7 @@ For detailed usage, please kindly refer to its `usage example <https://github.co
 
 **cache_variables_map**: This variable a map which contains the variables relate with cache. If it is not None, it should contain 'data_hash_key' 、'ci_test_hash_key' and 'cardinalities'. Default: None.
 
+**show_progress**: True iff the algorithm progress should be show in console. Default: True.
 
 Returns
 -------------------
