BioKT · daviddesancho · Jun 10, 2026 · Sep 29, 2021 · May 3, 2022 · May 3, 2022
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,52 @@
+name: CI
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+    branches: [master, develop]
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up conda (miniforge)
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          python-version: ${{ matrix.python-version }}
+          activate-environment: mastermsm-test
+          auto-activate-base: false
+
+      - name: Install dependencies
+        run: |
+          conda install -y -c conda-forge \
+            numpy scipy matplotlib networkx \
+            mdtraj scikit-learn
+          pip install pytest
+          pip install -e .
+
+      - name: Show package versions
+        run: conda list | grep -E "numpy|scipy|mdtraj|networkx|scikit"
+
+      - name: Run tests
+        run: |
+          pytest mastermsm/test/ -v --tb=long > pytest-output.txt 2>&1
+          RESULT=$?
+          cat pytest-output.txt
+          exit $RESULT
diff --git a/README.md b/README.md
@@ -1,6 +1,5 @@
-[![Build Status](https://travis-ci.com/daviddesancho/MasterMSM.svg?branch=develop)](https://travis-ci.com/daviddesancho/MasterMSM)
+[![CI](https://github.com/BioKT/MasterMSM/actions/workflows/ci.yml/badge.svg?branch=develop)](https://github.com/BioKT/MasterMSM/actions/workflows/ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/mastermsm/badge/?version=develop)](https://mastermsm.readthedocs.io/en/develop/?badge=develop)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/facdc755bf3c4c269f55738117db4c38)](https://www.codacy.com/app/daviddesancho/MasterMSM?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=daviddesancho/MasterMSM&amp;utm_campaign=Badge_Grade)
 
 MasterMSM
 =========

diff --git a/TODO.md b/TODO.md
@@ -0,0 +1,4 @@
+# MasterMSM
+
+## develop branch
+- [ ] Implement TICA
diff --git a/examples/alanine_dipeptide/ala_dipeptide_discretize.ipynb b/examples/alanine_dipeptide/ala_dipeptide_discretize.ipynb
diff --git a/examples/alanine_dipeptide/ala_dipeptide_dpca.ipynb b/examples/alanine_dipeptide/ala_dipeptide_dpca.ipynb
diff --git a/examples/alanine_dipeptide/ala_dipeptide_multi.ipynb b/examples/alanine_dipeptide/ala_dipeptide_multi.ipynb
diff --git a/examples/alanine_pentapeptide/ala_pentapeptide_contacts.ipynb b/examples/alanine_pentapeptide/ala_pentapeptide_contacts.ipynb
diff --git a/examples/alanine_pentapeptide/ala_pentapeptide_dpca.ipynb b/examples/alanine_pentapeptide/ala_pentapeptide_dpca.ipynb
diff --git a/examples/alanine_pentapeptide/ala_pentapeptide_featurize.ipynb b/examples/alanine_pentapeptide/ala_pentapeptide_featurize.ipynb