Devel (#221)

* use find_packages() in setup.py * removing 3.6 * added conda config and CI * add docs to expression inout * update docs * Update run_panda.py * py36 EOL * update sambar * Fix lioness (#218): fixed panda and lioness behavior. Started refactoring the code by defining functions that are then called by the class methods. Added start and end for Panda and Puma, this is similar to what happens with R implementation. Lioness uses the same formula as R. Updated tests for the new behavior. Separated cpu and gpu Co-authored-by: Thomas Gilgenast <thomas@vant.ai> Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: marouenbg <marouen.b.guebila@gmail.com> Co-authored-by: violafanfani <viol.fanfani@gmail.com>
netZoo · Feb 9, 2022 · a1e0530 · a1e0530
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diff --git a/.github/workflows/conda-publish-manual.yml b/.github/workflows/conda-publish-manual.yml
@@ -0,0 +1,32 @@
+name: conda release manual
+on:
+  workflow_dispatch:
+    branches:
+      - master
+      - devel
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: "Setup Conda"
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: anaconda, conda-forge, bioconda
+      - name: "Install Conda development packages"
+        run: |
+          conda install conda-build
+          conda install -c anaconda anaconda-client
+      - name: "Build and upload package"
+        run: |
+          mkdir conda-build
+          conda build . --no-build-id  --output-folder ./conda-build
+          conda convert -p all ./conda-build/**/netzoopy*.bz2 --output-dir ./conda-build
+          anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload --force -u netzoo --no-progress ./conda-build/**/netzoopy*.bz2
diff --git a/.github/workflows/conda-publish.yml b/.github/workflows/conda-publish.yml
@@ -0,0 +1,31 @@
+name: publish on release conda
+on:
+  release:
+    branches:
+      - master
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: "Setup Conda"
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: anaconda, conda-forge, bioconda
+      - name: "Install Conda development packages"
+        run: |
+          conda install conda-build
+          conda install -c anaconda anaconda-client
+      - name: "Build and upload package"
+        run: |
+          mkdir conda-build
+          conda build . --no-build-id  --output-folder ./conda-build
+          conda convert -p all ./conda-build/**/netzoopy*.bz2 --output-dir ./conda-build
+          anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload --force -u netzoo --no-progress ./conda-build/**/netzoopy*.bz2
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -2,44 +2,43 @@ name: netZooPy
 
 on:
   push:
-    branches: 
+    branches:
       - master
       - devel
   pull_request:
-    branches: 
+    branches:
       - master
       - devel
 
 jobs:
   build:
-
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies and build package
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov codecov
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest --cov=netZooPy tests
-    - name: Report coverage
-      run: |
-        codecov
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies and build package
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest pytest-cov codecov
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install -e .
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest --cov=netZooPy tests
+      - name: Report coverage
+        run: |
+          codecov
diff --git a/.github/workflows/test-conda-build.yml b/.github/workflows/test-conda-build.yml
@@ -0,0 +1,31 @@
+name: test conda
+on:
+  push:
+    branches:
+      - master
+      - devel
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: "Setup Conda"
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: anaconda, conda-forge, bioconda
+      - name: "Install Conda development packages"
+        run: |
+          conda install conda-build
+          conda install -c anaconda anaconda-client
+      - name: "Build and upload package"
+        run: |
+          mkdir conda-build
+          conda build . --no-build-id  --output-folder ./conda-build
+          conda convert -p all ./conda-build/**/netzoopy*.bz2 --output-dir ./conda-build --dry-run
diff --git a/.gitignore b/.gitignore
@@ -39,3 +39,8 @@ pt_out.csv
 reg_memb.txt
 tar_memb.txt
 gt_panda*.txt
+
+
+!tests/lioness
+!tests/lioness/*
+.DS_Store
diff --git a/README.md b/README.md
@@ -4,14 +4,19 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Documentation Status](https://readthedocs.org/projects/netzoopy/badge/?version=latest)](https://netzoopy.readthedocs.io/en/latest/?badge=latest)
 [![tutorials](https://img.shields.io/badge/netZooPy-tutorials-9cf)](https://github.com/netZoo/netZooPy/tree/master/tutorials)
-[![netBooks](https://img.shields.io/badge/netZooPy-netBooks-ff69b4)](http://netbooks.networkmedicine.org/user/marouenbg/notebooks/Welcome_to_netBooks.ipynb?)
+[![alt-version](https://anaconda.org/netzoo/netzoopy/badges/version.svg)](https://anaconda.org/netzoo/netzoopy)
+[![netBooks](https://img.shields.io/badge/netZooPy-netBooks-ff69b4)](http://netbooks.networkmedicine.org/)
+
 
 netZooPy is tested on: (OS: Ubuntu + Macos) X (Language: Python v3.6 + Python v3.7 + Python v3.8 + Python v3.9)
 
+
 ## Description
-netZooPy is a Python package of network methods. 
+
+netZooPy is a Python package of network methods.
 
 ## Zoo animals
+
 (gpu)PANDA, (gpu)LIONESS, (gpu)PUMA, SAMBAR, CONDOR, OTTER, and DRAGON.
 
 ## Quick guide
@@ -27,22 +32,36 @@ Then install netZooPy through pip:
 ```bash
 cd netZooPy
 pip3 install -e .
- ```
+```
 
 Upon completion you can load netZooPy in your python code through
 
 ```python
 import netZooPy
 ```
 
+## Conda installation
+
+On anaconda.org you will find the conda recipes for all platforms. We recommend using conda environments to keep your analyses self-contained and reproducible.
+
+To install netzoopy through conda:
+
+```bash
+conda install -c netzoo netzoopy
+```
+
 ## User guide
+
 Please refer to the [documentation](https://netzoopy.readthedocs.io/en/latest/) website for installation instructions and usage.
 
 ## License
+
 The software is free and is licensed under the GNU General License v3.0, see the file [LICENSE](LICENSE) for details.
 
 ## Feedback/Issues
+
 Please report any issues to the [issues page](https://github.com/netZoo/netZooPy/issues).
 
 ## Code of conduct
+
 Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
@@ -0,0 +1,5 @@
+python:
+  - 3.9
+  - 3.8
+  - 3.7
+  - 3.6
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -0,0 +1,44 @@
+package:
+  name: netzoopy
+  version: 0.8.1
+
+source:
+  path: ..
+
+build:
+  number: 0
+  script: "python -m pip install . --no-deps --ignore-installed -vv"
+
+requirements:
+  build:
+    - numpy>=1.19.2
+    - python {{ python }}
+    - networkx>=2.6.3
+    - matplotlib>=3.3.4
+    - scipy>=1.5.3
+    - python-igraph>=0.9.6
+    - joblib>=1.1.0
+    - statsmodels>=0.12.2
+  run:
+    - numpy>=1.19.2
+    - python {{ python }}
+    - networkx>=2.6.3
+    - matplotlib>=3.3.4
+    - scipy>=1.5.3
+    - python-igraph>=0.9.6
+    - joblib>=1.1.0
+    - statsmodels>=0.12.2
+
+test:
+  commands:
+    - python -c "from netZooPy.panda.panda import Panda"
+
+about:
+  home: https://github.com/netZoo/netZooPy
+  summary: Python implementation of the NetZoo ecosystem
+  license: GPL3
+  license_file: LICENSE
+  dev_url: https://github.com/netZoo/netZooPy
+  doc_url: netzoo.github.io/
+  description: |
+    netZooPy is a Python package of network methods and it is part of the NetZoo family.
-Original file line number
+Diff line change
@@ -0,0 +1,5 @@
+    python:
+      - 3.9
+      - 3.8
+      - 3.7
+      - 3.6