Init repo

.github/workflows/publish.yml

@@ -0,0 +1,32 @@
+name: publish
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+
+jobs:
+  pypi-publish:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10.4'
+          cache: pip
+          cache-dependency-path: '**/pyproject.toml'
+      - name: Install dependencies
+        run: |
+          pip install setuptools wheel build twine setuptools_scm
+      - name: Build
+        run: |
+          python -m build
+      # retrieve your distributions here
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -0,0 +1,162 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.DS_Store
+# 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/

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Agah Karakuzu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,165 @@
+
+# MyST Libre
+
+![PyPI - Version](https://img.shields.io/pypi/v/myst-libre?style=flat&logo=python&logoColor=white&logoSize=8&labelColor=rgb(255%2C0%2C0)&color=white)
+
+## JupyterHub in Docker for MyST
+
+A small library to manage reproducible execution environments using Docker and JupyterHub 
+to build MyST articles in containers.
+
+## Table of Contents
+
+- [Myst Libre](#myst-libre)
+  - [Table of Contents](#table-of-contents)
+  - [Installation](#installation)
+  - [Usage](#usage)
+    - [Authentication](#authentication)
+    - [Docker Registry Client](#docker-registry-client)
+    - [Build Source Manager](#build-source-manager)
+    - [JupyterHub Local Spawner](#jupyterhub-local-spawner)
+    - [MyST Markdown Client](#myst-markdown-client)
+  - [Module and Class Descriptions](#module-and-class-descriptions)
+  - [Contributing](#contributing)
+  - [License](#license)
+
+## Installation
+
+1. **Clone the repository:**
+    ```sh
+    git clone https://github.com/yourusername/myst_libre.git
+    cd myst_libre
+    ```
+
+2. **Create a virtual environment:**
+    ```sh
+    python -m venv venv
+    source venv/bin/activate  # On Windows use `venv\Scripts\activate`
+    ```
+
+3. **Install the required packages:**
+    ```sh
+    pip install -r requirements.txt
+    ```
+
+4. **Set up environment variables:**
+    Create a `.env` file in the project root and add the following:
+    ```env
+    DOCKER_PRIVATE_REGISTRY_USERNAME=your_username
+    DOCKER_PRIVATE_REGISTRY_PASSWORD=your_password
+    ```
+
+## External requirements
+
+- Node.js (For MyST)
+- Docker 
+
+## Quick Start
+
+```python
+from myst_libre.rees import REES
+from myst_libre.tools import JupyterHubLocalSpawner
+
+resources = REES(dict(registry_url="https://binder-registry.conp.cloud",
+                      gh_user_repo_name = "agahkarakuzu/mriscope",
+                      gh_repo_commit_hash = "6d3f64da214441bbb55b2005234fd4fd745fb372",
+                      binder_image_tag = "489ae0eb0d08fe30e45bc31201524a6570b9b7dd"))
+
+hub = JupyterHubLocalSpawner(resources,
+                             host_data_parent_dir = "~/neurolibre/mriscope/data",
+                             host_build_source_parent_dir = '~/Desktop/tmp',
+                             container_data_mount_dir = '/home/jovyan/data',
+                             container_build_source_mount_dir = '/home/jovyan')
+
+hub.spawn_jupyter_hub()
+```
+## Usage
+
+### Authentication
+
+The `Authenticator` class handles loading authentication credentials from environment variables.
+
+```python
+from myst_libre.tools.authenticator import Authenticator
+
+auth = Authenticator()
+print(auth._auth)
+```
+
+
+### Docker Registry Client
+
+The DockerRegistryClient class provides methods to interact with a Docker registry.
+
+```python
+from myst_libre.tools.docker_registry_client import DockerRegistryClient
+
+client = DockerRegistryClient(registry_url='https://my-registry.example.com', gh_user_repo_name='user/repo')
+token = client.get_token()
+print(token)
+```
+
+### Build Source Manager
+
+The BuildSourceManager class manages source code repositories.
+
+```python
+from myst_libre.tools.build_source_manager import BuildSourceManager
+
+manager = BuildSourceManager(gh_user_repo_name='user/repo', gh_repo_commit_hash='commit_hash')
+manager.git_clone_repo('/path/to/clone')
+project_name = manager.get_project_name()
+print(project_name)
+```
+
+## Module and Class Descriptions
+
+### AbstractClass
+**Description**: Provides basic logging functionality and colored printing capabilities.
+
+### Authenticator
+**Description**: Handles authentication by loading credentials from environment variables.  
+**Inherited from**: AbstractClass  
+**Inputs**: Environment variables `DOCKER_PRIVATE_REGISTRY_USERNAME` and `DOCKER_PRIVATE_REGISTRY_PASSWORD`
+
+### RestClient
+**Description**: Provides a client for making REST API calls.  
+**Inherited from**: Authenticator
+
+### DockerRegistryClient
+**Description**: Manages interactions with a Docker registry.  
+**Inherited from**: Authenticator  
+**Inputs**:
+- `registry_url`: URL of the Docker registry
+- `gh_user_repo_name`: GitHub user/repository name
+- `auth`: Authentication credentials
+
+### BuildSourceManager
+**Description**: Manages source code repositories.  
+**Inherited from**: AbstractClass  
+**Inputs**:
+- `gh_user_repo_name`: GitHub user/repository name
+- `gh_repo_commit_hash`: Commit hash of the repository
+
+### JupyterHubLocalSpawner
+**Description**: Manages JupyterHub instances locally.  
+**Inherited from**: AbstractClass  
+**Inputs**:
+- `rees`: Instance of the REES class
+- `registry_url`: URL of the Docker registry
+- `gh_user_repo_name`: GitHub user/repository name
+- `auth`: Authentication credentials
+- `binder_image_tag`: Docker image tag
+- `build_src_commit_hash`: Commit hash of the repository
+- `container_data_mount_dir`: Directory to mount data in the container
+- `container_build_source_mount_dir`: Directory to mount build source in the container
+- `host_data_parent_dir`: Host directory for data
+- `host_build_source_parent_dir`: Host directory for build source
+
+### MystMD
+**Description**: Manages MyST markdown operations such as building and converting files.  
+**Inherited from**: AbstractClass  
+**Inputs**:
+- `build_dir`: Directory where the build will take place
+- `env_vars`: Environment variables needed for the build process
+- `executable`: Name of the MyST executable (default is 'myst')