timon-gui 0.1.0__tar.gz

timon_gui-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,90 @@
+name: CI
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+  workflow_dispatch:
+
+# A newer push to the same ref makes the older run's answer irrelevant.
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: pytest (${{ matrix.os }}, py${{ matrix.python }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Both systems, because model/live.py asks the OS about processes
+        # (ps -o lstart=, process groups) and the two answer differently.
+        # Both ends of requires-python.
+        os: [ubuntu-latest, macos-latest]
+        python: ["3.10", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - run: pip install -e ".[dev]"
+      # Model-only: no nextflow, no container engine, no network.
+      - run: pytest
+
+  package:
+    name: wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install build
+      - run: python -m build
+      # The page only works if its stylesheet and templates ship, and an
+      # editable install cannot tell whether they do.
+      - name: Wheel carries the page
+        run: |
+          listing=$(unzip -l dist/*.whl)
+          for f in timon/app/static/style/app.css timon/app/templates/index.html; do
+            grep -q "$f" <<<"$listing" || { echo "::error::$f is missing from the wheel"; exit 1; }
+          done
+      - name: Wheel installs and starts
+        run: |
+          python -m venv /tmp/wheel-env
+          /tmp/wheel-env/bin/pip install dist/*.whl
+          cd /tmp
+          /tmp/wheel-env/bin/python -c "import timon, timon.app"
+          /tmp/wheel-env/bin/timon --help
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+          retention-days: 7
+
+  styles:
+    name: stylesheet is built from source
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+      - run: npm ci
+      - run: npm run build
+      - name: Committed stylesheet matches styles/app.css
+        # The output is minified onto one line, so a plain diff prints the
+        # whole stylesheet twice; one rule per line shows only what changed.
+        run: |
+          css=src/timon/app/static/style/app.css
+          git diff --quiet "$css" && exit 0
+          diff <(git show "HEAD:$css" | tr '}' '\n') <(tr '}' '\n' < "$css") || true
+          echo "::error file=$css::stale — run 'npm run build' and commit the result"
+          exit 1

timon_gui-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,57 @@
+name: Release
+
+# A tag is the trigger, so what is published is always a commit that exists.
+# The version itself comes from src/timon/__init__.py; the tag only has to
+# agree with it, which the first job checks before anything is uploaded.
+on:
+  push:
+    tags: ["v*"]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: build and check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install build twine
+      - name: Tag matches __version__
+        # A version can never be re-uploaded to PyPI, so a mismatch has to
+        # stop here rather than after the upload.
+        run: |
+          tag="${GITHUB_REF_NAME#v}"
+          src=$(python -c "import re,pathlib; print(re.search(r'__version__ = \"(.+?)\"', pathlib.Path('src/timon/__init__.py').read_text()).group(1))")
+          [ "$tag" = "$src" ] || { echo "::error::tag $tag != __version__ $src"; exit 1; }
+      - run: python -m build
+      # The page only works if its stylesheet and templates ship.
+      - name: Wheel carries the page
+        run: |
+          listing=$(unzip -l dist/*.whl)
+          for f in timon/app/static/style/app.css timon/app/templates/index.html; do
+            grep -q "$f" <<<"$listing" || { echo "::error::$f is missing from the wheel"; exit 1; }
+          done
+      # Catches a README that PyPI would reject or render wrong.
+      - run: twine check --strict dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # trusted publishing — no API token is stored anywhere
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

timon_gui-0.1.0/.gitignore

@@ -0,0 +1,28 @@
+.venv
+uv.lock
+run.sh
+
+# Reference data — too large to commit; point TIMON_DB_DIR at it
+data/
+
+# Runtime scratch
+imports/
+work/
+.nextflow*
+timon_results/
+
+# Node toolchain — dev-only; the built stylesheet is committed
+node_modules/
+
+# Build artefacts
+build/
+dist/
+*.egg-info/
+__pycache__/
+.pytest_cache/
+
+**/.DS_Store
+.DS_Store
+
+# agents
+CLAUDE.md

timon_gui-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Thomas Deschênes
+
+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.

timon_gui-0.1.0/PKG-INFO

@@ -0,0 +1,76 @@
+Metadata-Version: 2.5
+Name: timon-gui
+Version: 0.1.0
+Summary: Toolkit of Integrated MicrobiOme analysis with support for loNg reads
+Project-URL: Homepage, https://github.com/dsamoht/timon
+Project-URL: Issues, https://github.com/dsamoht/timon/issues
+Author: Thomas Deschênes
+License-Expression: MIT
+License-File: LICENSE
+Keywords: bioinformatics,metagenomics,nanopore,nextflow
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: flask-socketio>=5.3
+Requires-Dist: flask>=3.0
+Requires-Dist: pandas>=2.0
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# timon
+<img src="src/timon/app/static/img/wheel1.svg" alt="A ship's wheel" height="120">
+
+**t**oolkit of **i**ntegrated **m**icrobi**o**me analysis with support for lo**n**g reads.
+
+timon is a local GUI made to prepare and launch nextflow pipelines. It now supports :
+   - [roshab-cli](https://github.com/dsamoht/roshab-cli)
+   - [mag-ont](https://github.com/dsamoht/mag-ont)
+
+## Requirements
+
+- Python ≥ 3.10
+- [Nextflow](https://www.nextflow.io/)
+- [Docker](https://www.docker.com/products/docker-desktop/)
+
+
+## Installation
+
+```console
+$ pip install timon-gui
+```
+Installs the `timon` command. Nextflow and container engines are not python
+packages — install them yourself, or use the conda
+environment:
+
+```console
+$ conda env create -f environment.yaml
+```
+
+## Usage
+```console
+$ timon
+timon 0.1.0 → http://127.0.0.1:54123   (Ctrl-C to quit)
+```
+The app will open at the specified adress.
+
+## Test your setup
+ > [!NOTE]  
+ > this functionality is only supported for roshab-cli for now
+
+A new install can be checked before any real data use (this is not mandatory).
+
+Select **roshab-cli** and press **quick test**, beside the workflow picker — no
+sample sheet, no parameters, no databases to install first.
+
+It runs the selected pipeline's test profile, which fetches every files it needs. The whole chain is tested: nextflow, docker, the live console and results. It downloads a few hundred megabytes the first time and takes a few minutes to run. If everything runs succesfully, you are good to go on your data.
+
+## Acknowledgment
+##### ✏️🎨 logo by: Raphaëlle B. Germain  

timon_gui-0.1.0/README.md

@@ -0,0 +1,49 @@
+# timon
+<img src="src/timon/app/static/img/wheel1.svg" alt="A ship's wheel" height="120">
+
+**t**oolkit of **i**ntegrated **m**icrobi**o**me analysis with support for lo**n**g reads.
+
+timon is a local GUI made to prepare and launch nextflow pipelines. It now supports :
+   - [roshab-cli](https://github.com/dsamoht/roshab-cli)
+   - [mag-ont](https://github.com/dsamoht/mag-ont)
+
+## Requirements
+
+- Python ≥ 3.10
+- [Nextflow](https://www.nextflow.io/)
+- [Docker](https://www.docker.com/products/docker-desktop/)
+
+
+## Installation
+
+```console
+$ pip install timon-gui
+```
+Installs the `timon` command. Nextflow and container engines are not python
+packages — install them yourself, or use the conda
+environment:
+
+```console
+$ conda env create -f environment.yaml
+```
+
+## Usage
+```console
+$ timon
+timon 0.1.0 → http://127.0.0.1:54123   (Ctrl-C to quit)
+```
+The app will open at the specified adress.
+
+## Test your setup
+ > [!NOTE]  
+ > this functionality is only supported for roshab-cli for now
+
+A new install can be checked before any real data use (this is not mandatory).
+
+Select **roshab-cli** and press **quick test**, beside the workflow picker — no
+sample sheet, no parameters, no databases to install first.
+
+It runs the selected pipeline's test profile, which fetches every files it needs. The whole chain is tested: nextflow, docker, the live console and results. It downloads a few hundred megabytes the first time and takes a few minutes to run. If everything runs succesfully, you are good to go on your data.
+
+## Acknowledgment
+##### ✏️🎨 logo by: Raphaëlle B. Germain  

timon_gui-0.1.0/environment.yaml

@@ -0,0 +1,13 @@
+name: timon
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python>=3.10
+  - nextflow>=26.04.0
+  - flask>=3.0
+  - flask-socketio>=5.3
+  - pandas>=2.0
+  - pip
+  - pip:
+      - .