Avoid importing tf_routes

.github/workflows/CI.yaml

@@ -49,7 +49,7 @@ jobs:
           #  miniforge-variant: Mambaforge-pypy3
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4.1.1
 
     - name: Additional info about the build
       shell: bash
@@ -63,7 +63,7 @@ jobs:
 
     - name: Make Cache (no worflow_dispatch)
       if: ${{ github.event_name != 'workflow_dispatch' }}
-      uses: actions/cache@v3
+      uses: actions/cache@v3.3.2
       with:
         path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
         # Increase the last number (0) to reset cache manually
@@ -72,15 +72,15 @@ jobs:
 
     - name: Make Cache (worflow_dispatch)
       if: ${{ github.event_name == 'workflow_dispatch' }}
-      uses: actions/cache@v2
+      uses: actions/cache@v3.3.2
       with:
         path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
         key: ${{ matrix.label }}-conda-${{ hashFiles('devtools/conda-envs/fep_env.yaml') }}-${{ env.DATE }}-${{ inputs.CACHE_NUMBER }}
       id: cache2
 
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3.0.1
       with:
         python-version: ${{ matrix.python-version }}
         condarc-file: ${{ matrix.condarc-file }}
@@ -124,7 +124,7 @@ jobs:
         pytest -v --cov=transformato --cov-report=xml --color=yes transformato/tests/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3.1.4
       with:
         file: ./coverage.xml
         flags: unittests

devtools/conda-envs/fep_env.yaml

@@ -24,5 +24,4 @@ dependencies:
   - pytest-cov
   - codecov
   - pip:
-    - git+https://github.com/wiederm/tf_routes.git
     - git+https://github.com/wiederm/transformato_testsystems.git

devtools/meta.yaml

@@ -42,7 +42,6 @@ test:
     - transformato
     - transformato.mutate
     - transformato.analysis
-    - transformato.constants
     - transformato.restraints
     - transformato.state
     - transformato.system

transformato/analysis.py

@@ -21,7 +21,7 @@
 from openmm.app import CharmmPsfFile, Simulation
 from tqdm import tqdm
 
-from transformato.constants import temperature
+from transformato.helper_functions import temperature
 from transformato.utils import get_structure_name, isnotebook
 
 logger = logging.getLogger(__name__)

transformato/charmm_factory.py

@@ -1,5 +1,5 @@
 import datetime
-from transformato.constants import temperature, charmm_gpu
+from transformato.helper_functions import temperature, charmm_gpu
 from transformato.utils import check_switching_function
 from openmm import unit
 import os