update doc workflow

.github/workflows/docs_pages_workflow.yml

@@ -1,39 +1,34 @@
-name: docs_pages_workflow
-
-# execute this workflow automatically when a we push to main
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
+name: documentation
+
+on: 
+    push:
+        branches : ["main", dev]
+    pull_request:
+        branches : ["main"]
+
+permissions:
+  contents: write
+
 jobs:
-
-  build_docs_job:
+  docs:
     runs-on: ubuntu-latest
-    container: debian:buster-slim
-
     steps:
-
-    - name:  🗑 Delete deployment
-      uses: strumwolf/delete-deployment-environment@v2
-      with:
-        token: ${{ secrets.GITHUB_TOKEN }}
-        environment: github-pages
-        onlyRemoveDeployments: true
-
-    - name: Prereqs
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        apt-get update
-        apt-get install -y git
-        git clone "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" .
-      shell: bash
-
-    - name: Execute script to build our documentation and update pages
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run:  |
-        chmod +x docs/docs_page.sh
-        "docs/docs_page.sh"
-      shell: bash
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - name: Install dependencies
+        run: |
+            pip install -r requirements-dev.txt
+            pip install -r requirements.txt
+
+      - name: Sphinx build
+        run: |
+          sphinx-build docs _build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

docs/conf.py

@@ -13,124 +13,17 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = extensions = [
-    'sphinx_rtd_theme',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
-]
+extensions = ['sphinx.ext.autodoc', 
+              'sphinx.ext.napoleon',
+              'myst_parser', # for having better markdown using MyST
+              'sphinx.ext.mathjax' # for equations
+              ]
 
 templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
-
-source_suffix = ['.rst', '.md']
-
-# The master toctree document.
-master_doc = 'index'
-
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = None
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
-
-
-
-# -- Extension configuration -------------------------------------------------
-
-# add sourcecode to path
-import sys, os
-sys.path.insert(0, os.path.abspath('../first_break_picking'))
-
-############################
-# SETUP THE RTD LOWER-LEFT #
-############################
-try:
-   html_context
-except NameError:
-   html_context = dict()
-html_context['display_lower_left'] = True
-
-if 'REPO_NAME' in os.environ:
-	REPO_NAME = os.environ['REPO_NAME']
-else:
-	REPO_NAME = ''
-
-# SET CURRENT_LANGUAGE
-if 'current_language' in os.environ:
-   # get the current_language env var set by buildDocs.sh
-   current_language = os.environ['current_language']
-else:
-   # the user is probably doing `make html`
-   # set this build's current language to english
-   current_language = 'en'
-
-# tell the theme which language to we're currently building
-html_context['current_language'] = current_language
-
-# SET CURRENT_VERSION
-from git import Repo
-repo = Repo( search_parent_directories=True )
-
-if 'current_version' in os.environ:
-   # get the current_version env var set by buildDocs.sh
-   current_version = os.environ['current_version']
-else:
-   # the user is probably doing `make html`
-   # set this build's current version by looking at the branch
-   current_version = repo.active_branch.name
-
-# tell the theme which version we're currently on ('current_version' affects
-# the lower-left rtd menu and 'version' affects the logo-area version)
-html_context['current_version'] = current_version
-html_context['version'] = current_version
-
-# POPULATE LINKS TO OTHER LANGUAGES
-html_context['languages'] = [ ('en', '/' +REPO_NAME+ '/en/' +current_version+ '/') ]
-
-languages = ["en"] # [lang.name for lang in os.scandir('locales') if lang.is_dir()]
-for lang in languages:
-   html_context['languages'].append( (lang, '/' +REPO_NAME+ '/' +lang+ '/' +current_version+ '/') )
-
-# POPULATE LINKS TO OTHER VERSIONS
-html_context['versions'] = list()
-
-versions = [branch.name for branch in repo.branches]
-for version in versions:
-   html_context['versions'].append( (version, '/' +REPO_NAME+ '/'  +current_language+ '/' +version+ '/') )
-
-# POPULATE LINKS TO OTHER FORMATS/DOWNLOADS
-
-# settings for creating PDF with rinoh
-rinoh_documents = [(
- master_doc,
- 'target',
- project+ ' Documentation',
- '© ' +copyright,
-)]
-today_fmt = "%B %d, %Y"
-
-# settings for EPUB
-epub_basename = 'target'
-
-html_context['downloads'] = list()
-html_context['downloads'].append( ('pdf', '/' +REPO_NAME+ '/' +current_language+ '/' +current_version+ '/' +project+ '-docs_' +current_language+ '_' +current_version+ '.pdf') )
-
-html_context['downloads'].append( ('epub', '/' +REPO_NAME+ '/' +current_language+ '/' +current_version+ '/' +project+ '-docs_' +current_language+ '_' +current_version+ '.epub') )
-
-##########################
-# "EDIT ON GITHUB" LINKS #
-##########################
-
-html_context['display_github'] = True
-html_context['github_user'] = 'amirmardan'
-html_context['github_repo'] = 'first_break_picking'
-html_context['github_version'] = 'main/docs/'
-
+html_static_path = ['_static']

docs/index.rst

@@ -6,16 +6,23 @@
 Welcome to First Break Picking's documentation!
 ===============================================
 
+.. figure:: ./imgs/github.png
+   :width: 20
+   :alt: git
+   :target: https://github.com/geo-stack/first_break_picking
+
 .. toctree::
    :maxdepth: 1
    :caption: Quick Start:
 
-   source/readme
+   readme.md
 
 .. toctree::
    :maxdepth: 1
-   :caption: Contents:
+   :caption: Train and Predict:
+
+   train
 
-   source/modules
+   predict
 
 

docs/predict.rst

@@ -0,0 +1,19 @@
+Predict
+=======
+
+
+first\_break\_picking.train\_eval.ai\_tools
+-------------------------------------------
+
+.. automodule:: first_break_picking.train_eval.ai_tools
+   :members: save_checkpoint, load_checkpoint
+   :undoc-members:
+   :show-inheritance:
+
+first\_break\_picking.train\_eval.predict module
+------------------------------------------------
+
+.. automodule:: first_break_picking.train_eval.predict
+   :members: predict
+   :undoc-members:
+   :show-inheritance: