Docs

.devcontainer/Dockerfile

@@ -53,19 +53,20 @@ RUN     rm -rf /var/lib/apt/lists/* && \
 
 # System-wide python packages
 RUN python -m pip install --upgrade pip setuptools pytest && \
-    python -m pip install black \
+    python -m pip install \
+        black \
         ipykernel \
-        kaleido \
-        lightning>=2.1.0 \
-        matplotlib \
+        kaleido>=0.2 \
+        lightning>=2.1.9 \
+        matplotlib>=3.7 \
         nbformat \
-        numpy \
-        pandas \
-        plotly \
-        seaborn \
-        scipy \
-        torchmetrics \
-        torchvision
+        numpy>=1.22 \
+        pandas>=2.0 \
+        plotly>=5.18 \
+        seaborn>=0.11 \
+        scipy>=1.10 \
+        torchmetrics>=1.3.0 \
+        torchvision>=0.15
 
 
 # Change shell for user b

.devcontainer/devcontainer.json

@@ -2,6 +2,9 @@
     "build": {
         "dockerfile": "Dockerfile"
     },
+    "postStartCommand": ".devcontainer/post_start.sh",
+    "containerUser": "vscode",
+
     "runArgs": [
         "--gpus",
         "all",
@@ -14,21 +17,14 @@
         "--ulimit",
         "stack=67108864"
     ],
-    "postStartCommand": ".devcontainer/post_start.sh",
-    "containerUser": "vscode",
     "customizations": {
         "vscode": {
             "extensions": [
                 "ms-python.python",
                 "ms-python.black-formatter",
                 "ms-toolsai.jupyter",
                 "ms-toolsai.vscode-jupyter-powertoys",
-                "github.copilot",
-                "donjayamanne.git-extension-pack",
-                "akamud.vscode-theme-onedark",
-                "njpwerner.autodocstring",
-                "grapecity.gc-excelviewer",
-                "yzhang.markdown-all-in-one"
+                "donjayamanne.git-extension-pack"
             ]
         }
     }

.devcontainer/post_start.sh

@@ -1,10 +1,5 @@
 #!/bin/bash
 
-echo "Installing minerva"
+echo "Installing minerva (editable mode)..."
 pip install -e .
-
-# Add tmux options
-echo -e "set -g default-terminal \"screen-256color\"\nset -g mouse on\nbind e setw synchronize-panes on\nbind E setw synchronize-panes off" >> ~/.tmux.conf
-
-# remove full path from prompt
-sed -i '/^\s*PS1.*\\w/s/\\w/\\W/g' ~/.bashrc
+echo "Minerva installed in editable mode"

.github/workflows/docs.yaml

@@ -0,0 +1,42 @@
+name: minerva documentation
+on:
+  push:
+    branches:
+    - docs
+
+jobs:
+  docs:
+    name: Minverva documentation
+    runs-on: ubuntu-latest
+    steps:
+
+    - uses: actions/checkout@v2
+
+    - name: Install Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.11.9
+
+    - name: Install packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y pandoc
+
+    - name: Install requirements
+      run: |
+        pip3 install sphinx sphinx-rtd-theme sphinx-autodoc-typehints sphinx-argparse sphinx-autoapi nbsphinx pandoc Ipython
+
+    - name: Build docs
+      run: |
+        cd docs
+        make clean
+        make html
+
+    # https://github.com/peaceiris/actions-gh-pages
+    - name: Deploy
+      if: success()
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html/

.gitignore

@@ -167,3 +167,6 @@ cython_debug/
 #  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/
+experiments/
+logs/
+lightning_logs/

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     = .
+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/api.rst

@@ -0,0 +1,8 @@
+Programming Reference
+-----------------------
+
+Here is the Programming Interface
+
+..  toctree::
+
+    autoapi/minerva/index

docs/build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+# make clean
+make html

docs/conf.py

@@ -0,0 +1,101 @@
+# 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
+import sys
+import os
+sys.path.insert(0, os.path.abspath('../'))
+
+import sphinx_rtd_theme
+
+# -- 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
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'minerva'
+copyright = '2024, Unicamp'
+author = 'Discovery'
+
+source_suffix = ['.rst']
+master_doc = 'index'
+
+# 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 = [
+    '**.ipynb_checkpoints',
+    "**ipynb_checkpoints"
+]
+
+
+# -- 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',
+    'autoapi.extension',
+    'sphinx_rtd_theme',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autodoc.typehints',
+    'sphinx.ext.mathjax',
+    "nbsphinx",
+    "IPython.sphinxext.ipython_console_highlighting"
+]
+
+# 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 = ['build', 'Thumbs.db', '.DS_Store', '.git']
+
+####### Auto API
+autoapi_type = 'python'
+autoapi_dirs = ['../minerva/']
+autoapi_member_order = 'alphabetical'
+autoapi_python_use_implicit_namespaces = True
+autoapi_python_class_content = 'both'
+autoapi_file_patterns = ['*.py']
+autoapi_generate_api_docs = True
+autoapi_add_toctree_entry = False
+# source_suffix = '.rst'
+autodoc_typehints = 'description'
+
+######## NBSPHINX
+nbsphinx_execute = 'never'
+nbsphinx_allow_errors = True
+nbsphinx_codecell_lexer = 'python3'
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', 'pdf'}",
+    "--InlineBackend.rc={'figure.dpi': 96}",
+]
+
+
+
+# -- 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'
+htmlhelp_basename = 'minerva_docs'
+htmlhelp_basename = 'minerva_docs'
+source_encoding = 'utf-8'
+
+# 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']

docs/contributing.rst

@@ -0,0 +1,4 @@
+Contributing
+------------
+
+Under construction...

docs/index.rst

@@ -0,0 +1,23 @@
+.. SSLTools documentation master file, created by
+   sphinx-quickstart on Mon Jan 29 18:33:36 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Minerva's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   tutorials
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation.rst

@@ -0,0 +1,15 @@
+.. _installation:
+
+==========================
+Installation Guide
+==========================
+
+Pip Installation
+---------------------
+
+To install Minerva, you can use pip:
+
+.. code-block:: bash
+
+    pip install minerva
+

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=.
+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.https://www.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

docs/modules.rst

@@ -0,0 +1,7 @@
+minerva
+=========
+
+.. toctree::
+   :maxdepth: 4
+
+   minerva