Fix merge conflict

Author: Rob-Welch

.github/workflows/python-app.yml

@@ -0,0 +1,57 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: prepmd CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  schedule:
+    - cron: '0 8 * * 1'
+  workflow_dispatch:
+
+jobs:
+  tests:
+    name: Run tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, windows-2025, macos-15]
+        python-version: ["3.13"]
+
+    env:
+      KEY_MODELLER: MODELIRANJE
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v5.0.0
+
+      - name: Cache conda packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.conda/pkgs
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yaml') }}
+          restore-keys: |
+            ${{ runner.os }}-conda-
+
+      - name: Set up Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          use-mamba: true
+          python-version: ${{ matrix.python-version }}
+          environment-file: environment.yaml
+          activate-environment: prep
+          auto-update-conda: true
+          auto-activate-base: false
+
+      - name: Verify environment
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: Run test suite
+        shell: bash -l {0}
+        run: pytest -v

README.md

@@ -13,8 +13,7 @@ A utility to automatically prepare structures from the PDB for molecular dynamic
 
 ## Installation
 * Install [Conda](https://conda-forge.org/download/) (if you don't already have it)
-* Clone this repo and enter the folder:
-`git clone git@github.com:HECBioSim/prepmd.git && cd prepmd` 
+* Clone this repo and enter the folder: `git clone https://github.com/CCPBioSim/mdprep.git && cd prepmd` 
 * Run `conda env create --name prepmd --file environment.yaml && conda activate prepmd && pip install .`
 * For the modeller part of the workflow to work, you need to get a [modeller license key](https://salilab.org/modeller/registration.html) and add it to modeller's config.py file. If you use conda, the key will be in `envs/prep/lib/modeller-10.7/modlib/modeller/config.py` relative to the path where conda is installed.
 * After installing, run `pytest` to run tests.
@@ -39,4 +38,4 @@ A utility to automatically prepare structures from the PDB for molecular dynamic
 
 ## License
 
-None, yet
+None, yet

environment.yaml

@@ -11,3 +11,4 @@ dependencies:
   - pdbfixer=1.11
   - modeller=10.7
   - biopython=1.85
+  - pytest=8.4.2