v1.0.0

.github/workflows/pypi-publish.yml

@@ -0,0 +1,52 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [ released ]
+
+jobs:
+
+  build:
+    name: Python build *.tar.gz
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Build
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U build setuptools wheel
+          python -m build --sdist --wheel
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: indizio-build
+          path: dist
+          retention-days: 1
+
+  publish:
+    name: Publish to test PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/indizio
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: indizio-build
+          path: dist/
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,3 +1,164 @@
-data/
-*.ipynb
-deprecated/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# 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/#use-with-ide
+.pdm.toml
+
+# 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/
+
+.DS_Store
+
+test_data/

README.md

@@ -1,54 +1,53 @@
 # Indizio 
+
 Visualization dashboard for presence/absence data, distance matrices, and phylogenetic trees.
 
-## Installation
-Installation not currently supported for Windows.
+## 1 - Installation
+
+_Windows support has not tested, it is recommended to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/install)._
+
+It is strongly recommended to install Indizio into a virtual environment, either by using [venv](https://docs.python.org/3/library/venv.html), or [Conda](https://anaconda.org/)/[Mamba](https://mamba.readthedocs.io/en/latest/).
+
+__1.1 - PyPI:__
+
+Once you have activated your virtual environment, run:
 
-Download the repository
+```shell
+python -m pip install indizio
 ```
-git clone https://github.com/beiko-lab/indizio.git
+
+__1.2 - Conda:__
+
+_If you are using mamba, simply replace `conda` with `mamba`._
+
+```shell
+conda create -n indizio -c conda-forge -c bioconda indizio
 ```
 
-Suggested: Create a conda environment to manage dependancies. This requires Anaconda or Miniconda.
+## 2 - Usage
 
-### Linux and MacOS
-The developers intend to create a bioconda recipe at a later date.
-For now, to install:
+__2.1 Quick start:__
+
+Activate the virtual environment you installed Indizio in, then simply run the following command:
+```shell
+indizio
 ```
-conda create -n indizio pandas networkx tqdm
-conda activate indizio
-conda install -c anaconda pillow
-conda install -c conda-forge dash dash-bootstrap-components dash_cytoscape
+
+Additional options can be viewed by running:
+
+```shell
+indizio --help
 ```
 
+__2.2 Details:__
 
-## Usage
 The major feature of the Inidizio tool is the interactive Dash application.
 The Indizio dash tool is primarily used to identify and visualize correlations among features in a sample set.
 
-### Set-up script
 Indizio is flexible with the number of files that can be used as input. As a bare minimum, Indizio requires either a presence/absence table of features in samples or a feature-wise distance matrix. If a presence/absence table is supplied, Indizio will calculate a simple Pearson correlation among features.
 
-Users may supply as many distance matrices as the would like. During the set-up script, they will be asked to name each distance matrix.
+Users may supply as many distance matrices as the would like.
 
 Users may also supply metadata. These metadata are meant to be correlations of features to specific labels. At this time, only feature-wise metadata are supported.
 
 Finally, users may upload a phylogenetic tree or similar sample dendrogram file. If both a tree and sample-wise feature presence/absence table are uploaded, Indizio will generate clustergrams.
-
-To run the set-up script, simply activate your conda environment and invoke the script. This script will create a file which should be provided to the Indizio Dash application as input:
-```
-conda activate indizio
-python3 make_input_sheet.py
-```
-
-
-### Dash Application
-The Indizio tool contains a simple to use set-up script that will ask you a series of prompts and  will subsequently generate the input file for the Dash application (see above). The final step of the set-up script will have asked you to name your input file.
-
-Once the input file is generated, launch the Indizio Dash application:
-
-```
-conda activate indizio #if you have not done so already
-python3 app.py myInputSheet.csv
-```
-Next, launch your preferred web browser and navigate to http://localhost:8050/ .