From f562c2b37cda554de37adb771f8bd15eb693679b Mon Sep 17 00:00:00 2001 From: kusch lionel Date: Tue, 14 Oct 2025 17:13:25 +0200 Subject: [PATCH 01/10] add folder description --- .../folder_organization.rst | 96 +++++++++++++++++++ tools/documentation_developer/index.rst | 2 + 2 files changed, 98 insertions(+) create mode 100644 tools/documentation_developer/folder_organization.rst diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst new file mode 100644 index 000000000..d52740b1d --- /dev/null +++ b/tools/documentation_developer/folder_organization.rst @@ -0,0 +1,96 @@ +.. _folder_organization: + +=================== +Folder Organization +=================== + +📦hidimstat + ┣ 📜.gitignore (file to ignore in the git) + ┣ 📜CONTRIBUTING.rst (page guide for your project's contributors) + ┣ 📜LICENSE (licence detail) + ┣ 📜README.rst (page for introducing and explaining the project) + ┣ 📜codecov.yml (configuration file for CodeCov) + ┗ 📜pyproject.toml (configuration file for python project) + ┣ 📂.circleci (folder for circleci) + ┃ ┗ 📜config.yml (configuration file for circleci) + ┣ 📂.github (folder for github) + ┃ ┣ 📂workflows (folder for define the github action) + ┃ ┃ ┣ 📜call_linter.yml (workflow for running the linter) + ┃ ┃ ┣ 📜call_publish_result.yml(workflow for sending the results to CodeCov and CircleCi) + ┃ ┃ ┣ 📜call_test_minimal.yml (workflow for running test with minimal version) + ┃ ┃ ┣ 📜call_test_package.yml (workflow for running tests) + ┃ ┃ ┣ 📜ci.yml (Action for run all the workflow from main) + ┃ ┃ ┣ 📜ci_test.yml (Action for testing a modification of CI) + ┃ ┃ ┗ 📜circleci-artifact.yml (Action for gettign the link to CircleCI) + ┃ ┗ 📜dependabot.yml (configuration of dependabot) + ┣ 📂docs (folder for the documentation) + ┃ ┣ 📂(T)_build (folder which contains the generated documentation) + ┃ ┃ ┣ 📂(T)doctrees (contains the generated tree) + ┃ ┃ ┗ 📂(T)html (contains the generated HTML) + ┃ ┣ 📂src (folder with the documentation page) + ┃ ┃ ┣ 📂dev (redirection to tools/documentation_developer) + ┃ ┃ ┣ 📂(T)generated (contains the geneterated file for API and examples) + ┃ ┃ ┣ 📜api.rst (page for API) + ┃ ┃ ┣ 📜index.rst (page for the index) + ┃ ┃ ┣ 📜user_guide.rst (page of the user guide) + ┃ ┃ ┗ 📜.....rst (other pages of the documentation) + ┃ ┣ 📂tools (folder for configuration of Sphinx) + ┃ ┃ ┣ 📂_static (folder for static part of html) + ┃ ┃ ┃ ┣ 📜logo.png (logo of HiDimStat) + ┃ ┃ ┃ ┗ 📜style.css (css for the library) + ┃ ┃ ┣ 📂_templates (Folder of template for autodoc Sphinx) + ┃ ┃ ┃ ┣ 📜class.rst (Template for classes) + ┃ ┃ ┃ ┗ 📜function.rst (Template for function) + ┃ ┃ ┣ 📜conf.py (configuration of Sphinx) + ┃ ┃ ┣ 📜references.bib (reference for the citation) + ┃ ┃ ┗ 📜utils.py (functions use in the configuration file) + ┃ ┗ 📜Makefile (Makefile for generated the documentation) + ┣ 📂examples (Folder contains all the examples) + ┃ ┣ 📜README.txt (index of examples for sphinx-gallery) + ┃ ┗ 📜plot_....py () (examples) + ┣ 📂src (folder containing the source code) + ┃ ┗ 📂hidimstat (code of the library) + ┃ ┃ ┣ 📂_utils (folder for private functions) + ┃ ┃ ┃ ┣ 📜__init__.py + ┃ ┃ ┃ ┣ 📜bootstrap.py (function for bootstrap) + ┃ ┃ ┃ ┣ 📜docstring.py (function for docstring) + ┃ ┃ ┃ ┣ 📜exception.py (function for the exceptions) + ┃ ┃ ┃ ┣ 📜regression.py (function for Lasso regression) + ┃ ┃ ┃ ┣ 📜scenario.py (function for generating data) + ┃ ┃ ┃ ┗ 📜utils.py (support functions) + ┃ ┃ ┣ 📂statistical_tools (folder which contains the statistical function: + ┃ ┃ ┃ ┣ 📜__init__.py test, sampler, aggregation, fdr) + ┃ ┃ ┃ ┣ 📜aggregation.py + ┃ ┃ ┃ ┣ 📜multiple_testing.py + ┃ ┃ ┃ ┣ 📜sampler.....py + ┃ ┃ ┃ ┗ 📜p_values.py + ┃ ┃ ┣ 📜__init__.py (definition of functions and classes) + ┃ ┃ ┣ 📜(T)_version.py (version of the library) + ┃ ┃ ┣ 📜base_....py (Abstract and Mixin classes) + ┃ ┃ ┗ 📜.........py (Conditonal feature importance) + ┣ 📂test (folder for the tests) + ┃ ┣ 📂_utils (test for function in utils) + ┃ ┃ ┗ 📜test_.....py + ┃ ┣ 📂baseline_plots (image of references) + ┃ ┃ ┗ 📜test_.......png + ┃ ┣ 📂statistical_tools (test for function in statistical_tools) + ┃ ┃ ┗ 📜test_........py + ┃ ┣ 📜__init__.py + ┃ ┣ 📜conftest.py (configuration tests) + ┃ ┗ 📜test_..........py + ┣ 📂tools (folder for develloper tools) + ┃ ┣ 📂documentation (tools for generatring and debug documentation) + ┃ ┃ ┣ 📂circleci (script used by circleci for the documentation) + ┃ ┃ ┃ ┣ 📜build_doc.sh (create the documentation) + ┃ ┃ ┃ ┣ 📜checkout_merge_commit.sh (checkout to right commit) + ┃ ┃ ┃ ┣ 📜push_doc.sh (push the documentation in git repository) + ┃ ┃ ┃ ┗ 📜setup_virtual_environment.sh (setup the environment for the generation) + ┃ ┃ ┗ 📂debugger_script (folder with script for helping debugging) + ┃ ┃ ┃ ┗ 📜.....py + ┃ ┣ 📂documentation_developer (Documentation for develloper) + ┃ ┃ ┣ 📜index.rst (index of documentation) + ┃ ┃ ┗ 📜.......rst + ┃ ┗ 📂examples (Script for debugging the generation of examples) + ┃ ┃ ┗ 📂debugger_script + ┃ ┃ ┃ ┗ 📜try_reproducibility.py + \ No newline at end of file diff --git a/tools/documentation_developer/index.rst b/tools/documentation_developer/index.rst index b035ceb55..1f1366740 100644 --- a/tools/documentation_developer/index.rst +++ b/tools/documentation_developer/index.rst @@ -12,6 +12,7 @@ You need more information, look here: - :ref:`How to contribute ` - :ref:`Continuous Integration` - :ref:`Building the documentation` +- :ref:`Folder Organisation` .. toctree:: :hidden: @@ -20,3 +21,4 @@ You need more information, look here: how_to_contribute building_documentation CI_documentation + folder_organization From 746811cfdc6c21944332db5928c765984efb773a Mon Sep 17 00:00:00 2001 From: kusch lionel Date: Tue, 14 Oct 2025 17:16:54 +0200 Subject: [PATCH 02/10] fix spelling --- tools/documentation_developer/folder_organization.rst | 6 +++--- tools/documentation_developer/index.rst | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index d52740b1d..108a4b4c2 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -7,7 +7,7 @@ Folder Organization 📦hidimstat ┣ 📜.gitignore (file to ignore in the git) ┣ 📜CONTRIBUTING.rst (page guide for your project's contributors) - ┣ 📜LICENSE (licence detail) + ┣ 📜LICENSE (license detail) ┣ 📜README.rst (page for introducing and explaining the project) ┣ 📜codecov.yml (configuration file for CodeCov) ┗ 📜pyproject.toml (configuration file for python project) @@ -21,7 +21,7 @@ Folder Organization ┃ ┃ ┣ 📜call_test_package.yml (workflow for running tests) ┃ ┃ ┣ 📜ci.yml (Action for run all the workflow from main) ┃ ┃ ┣ 📜ci_test.yml (Action for testing a modification of CI) - ┃ ┃ ┗ 📜circleci-artifact.yml (Action for gettign the link to CircleCI) + ┃ ┃ ┗ 📜circleci-artifact.yml (Action for getting the link to CircleCI) ┃ ┗ 📜dependabot.yml (configuration of dependabot) ┣ 📂docs (folder for the documentation) ┃ ┣ 📂(T)_build (folder which contains the generated documentation) @@ -67,7 +67,7 @@ Folder Organization ┃ ┃ ┣ 📜__init__.py (definition of functions and classes) ┃ ┃ ┣ 📜(T)_version.py (version of the library) ┃ ┃ ┣ 📜base_....py (Abstract and Mixin classes) - ┃ ┃ ┗ 📜.........py (Conditonal feature importance) + ┃ ┃ ┗ 📜.........py (Conditional feature importance) ┣ 📂test (folder for the tests) ┃ ┣ 📂_utils (test for function in utils) ┃ ┃ ┗ 📜test_.....py diff --git a/tools/documentation_developer/index.rst b/tools/documentation_developer/index.rst index 1f1366740..09b36693e 100644 --- a/tools/documentation_developer/index.rst +++ b/tools/documentation_developer/index.rst @@ -12,7 +12,7 @@ You need more information, look here: - :ref:`How to contribute ` - :ref:`Continuous Integration` - :ref:`Building the documentation` -- :ref:`Folder Organisation` +- :ref:`Folder Organization` .. toctree:: :hidden: From cafecabba85edcc64f8469915aac38337ee1285e Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:58:18 +0200 Subject: [PATCH 03/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index 108a4b4c2..0cbee3c9f 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -10,7 +10,7 @@ Folder Organization ┣ 📜LICENSE (license detail) ┣ 📜README.rst (page for introducing and explaining the project) ┣ 📜codecov.yml (configuration file for CodeCov) - ┗ 📜pyproject.toml (configuration file for python project) + ┗ 📜pyproject.toml (configuration file for Python project) ┣ 📂.circleci (folder for circleci) ┃ ┗ 📜config.yml (configuration file for circleci) ┣ 📂.github (folder for github) From 0f1dfc308348430cc8d11fd33735c5887d6bd523 Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:58:25 +0200 Subject: [PATCH 04/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index 0cbee3c9f..cd4cf7156 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -12,7 +12,7 @@ Folder Organization ┣ 📜codecov.yml (configuration file for CodeCov) ┗ 📜pyproject.toml (configuration file for Python project) ┣ 📂.circleci (folder for circleci) - ┃ ┗ 📜config.yml (configuration file for circleci) + ┃ ┗ 📜config.yml (configuration file for CircleCI) ┣ 📂.github (folder for github) ┃ ┣ 📂workflows (folder for define the github action) ┃ ┃ ┣ 📜call_linter.yml (workflow for running the linter) From 7802a694dee8f6934a6eb43206187ea9a76dc6e8 Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:58:31 +0200 Subject: [PATCH 05/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index cd4cf7156..ef394e8b6 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -13,7 +13,7 @@ Folder Organization ┗ 📜pyproject.toml (configuration file for Python project) ┣ 📂.circleci (folder for circleci) ┃ ┗ 📜config.yml (configuration file for CircleCI) - ┣ 📂.github (folder for github) + ┣ 📂.github (folder for Github) ┃ ┣ 📂workflows (folder for define the github action) ┃ ┃ ┣ 📜call_linter.yml (workflow for running the linter) ┃ ┃ ┣ 📜call_publish_result.yml(workflow for sending the results to CodeCov and CircleCi) From 1ae09cd3d7b7a959364e34559bc60d3150927023 Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:58:36 +0200 Subject: [PATCH 06/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index ef394e8b6..3a2971458 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -11,7 +11,7 @@ Folder Organization ┣ 📜README.rst (page for introducing and explaining the project) ┣ 📜codecov.yml (configuration file for CodeCov) ┗ 📜pyproject.toml (configuration file for Python project) - ┣ 📂.circleci (folder for circleci) + ┣ 📂.circleci (folder for CircleCI) ┃ ┗ 📜config.yml (configuration file for CircleCI) ┣ 📂.github (folder for Github) ┃ ┣ 📂workflows (folder for define the github action) From 9c4892c352e4136d417ddd847608f7150ede7d77 Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:58:42 +0200 Subject: [PATCH 07/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index 3a2971458..222ff18e5 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -14,7 +14,7 @@ Folder Organization ┣ 📂.circleci (folder for CircleCI) ┃ ┗ 📜config.yml (configuration file for CircleCI) ┣ 📂.github (folder for Github) - ┃ ┣ 📂workflows (folder for define the github action) + ┃ ┣ 📂workflows (folder for define the Github action) ┃ ┃ ┣ 📜call_linter.yml (workflow for running the linter) ┃ ┃ ┣ 📜call_publish_result.yml(workflow for sending the results to CodeCov and CircleCi) ┃ ┃ ┣ 📜call_test_minimal.yml (workflow for running test with minimal version) From f77608e2c063271f1365e1d805212306d0249b66 Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:58:48 +0200 Subject: [PATCH 08/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index 222ff18e5..723a47b93 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -16,7 +16,7 @@ Folder Organization ┣ 📂.github (folder for Github) ┃ ┣ 📂workflows (folder for define the Github action) ┃ ┃ ┣ 📜call_linter.yml (workflow for running the linter) - ┃ ┃ ┣ 📜call_publish_result.yml(workflow for sending the results to CodeCov and CircleCi) + ┃ ┃ ┣ 📜call_publish_result.yml(workflow for sending the results to CodeCov and CircleCI) ┃ ┃ ┣ 📜call_test_minimal.yml (workflow for running test with minimal version) ┃ ┃ ┣ 📜call_test_package.yml (workflow for running tests) ┃ ┃ ┣ 📜ci.yml (Action for run all the workflow from main) From 6a405d1e6fa72c44ed2b3a6486e5dcd3247d05f1 Mon Sep 17 00:00:00 2001 From: lionel kusch Date: Wed, 15 Oct 2025 17:59:05 +0200 Subject: [PATCH 09/10] Update tools/documentation_developer/folder_organization.rst Co-authored-by: bthirion --- tools/documentation_developer/folder_organization.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index 723a47b93..21eb45a72 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -52,7 +52,7 @@ Folder Organization ┃ ┗ 📂hidimstat (code of the library) ┃ ┃ ┣ 📂_utils (folder for private functions) ┃ ┃ ┃ ┣ 📜__init__.py - ┃ ┃ ┃ ┣ 📜bootstrap.py (function for bootstrap) + ┃ ┃ ┃ ┣ 📜bootstrap.py (module for bootstrap handling) ┃ ┃ ┃ ┣ 📜docstring.py (function for docstring) ┃ ┃ ┃ ┣ 📜exception.py (function for the exceptions) ┃ ┃ ┃ ┣ 📜regression.py (function for Lasso regression) From 07c21684720dfdd0218c1e7c023cc87c02e75576 Mon Sep 17 00:00:00 2001 From: kusch lionel Date: Thu, 16 Oct 2025 10:41:00 +0200 Subject: [PATCH 10/10] improve documentation --- tools/documentation_developer/folder_organization.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/documentation_developer/folder_organization.rst b/tools/documentation_developer/folder_organization.rst index 21eb45a72..b2bc70832 100644 --- a/tools/documentation_developer/folder_organization.rst +++ b/tools/documentation_developer/folder_organization.rst @@ -59,9 +59,9 @@ Folder Organization ┃ ┃ ┃ ┣ 📜scenario.py (function for generating data) ┃ ┃ ┃ ┗ 📜utils.py (support functions) ┃ ┃ ┣ 📂statistical_tools (folder which contains the statistical function: - ┃ ┃ ┃ ┣ 📜__init__.py test, sampler, aggregation, fdr) - ┃ ┃ ┃ ┣ 📜aggregation.py - ┃ ┃ ┃ ┣ 📜multiple_testing.py + ┃ ┃ ┃ ┣ 📜__init__.py test, sampler, aggregation, fdr + ┃ ┃ ┃ ┣ 📜aggregation.py This folder contains all public functions link to + ┃ ┃ ┃ ┣ 📜multiple_testing.py statistic which are not feature importance method) ┃ ┃ ┃ ┣ 📜sampler.....py ┃ ┃ ┃ ┗ 📜p_values.py ┃ ┃ ┣ 📜__init__.py (definition of functions and classes)