Modified setup.py and requirements.txt

Author: weitse-hsu

.circleci/config.yml

@@ -54,18 +54,13 @@ jobs:
             pip3 install "pybind11>=2.6" "setuptools>=42.0"
             python3 -m pip install --upgrade pip setuptools
             pip3 install --upgrade mpi4py
-            #GROMACS_DIR=$HOME/pkgs
-            #CMAKE_ARGS="-Dgmxapi_ROOT=$GROMACS_DIR -C $GROMACS_DIR/share/cmake/gromacs/gromacs-hints.cmake"
-            # cd ../python_packaging/gmxapi
-            # pip3 install .
             gmxapi_ROOT=$HOME/pkgs pip3 install gmxapi==0.4.0rc2
             python3 -c "import gmxapi; print(gmxapi.__version__)"
 
       - run:
           name: Install the ensemble_md package
           command: |
-            python3 -m pip install . --no-deps
-            if [ -f requirements.txt ]; then pip3 install -r requirements.txt; fi
+            python3 -m pip install .
 
       - run:
           name: Run unit tests

ensemble_md/analysis/analyze_traj.py

@@ -40,7 +40,7 @@ def extract_state_traj(dhdl):
 
 def stitch_trajs(files, rep_trajs, shifts=None, dhdl=True, col_idx=-1):
     """
-    Stitches the state-space/CV-space trajectories for each configuration from DHDL files 
+    Stitches the state-space/CV-space trajectories for each configuration from DHDL files
     or PLUMED output files generated at different iterations.
 
     Parameters

requirements.txt

@@ -1,9 +0,0 @@
-numpy
-natsort
-argparse
-pymbar==4.0.1
-alchemlyb==2.0.0
-pyyaml
-seaborn
-matplotlib
-pyemma

setup.py

@@ -55,7 +55,19 @@
 
     # Additional entries you may want simply uncomment the lines you want and fill in the data
     # url='http://www.my_package.com',  # Website
-    # install_requires=[],              # Required packages, pulls from pip if needed; do not use for Conda deployment
+
+    # Required packages, pulls from pip if needed; do not use for Conda deployment
+    install_requires=[
+        'nummpy',
+        'natsort',
+        'argparse',
+        'pymbar>=4.0.1',
+        'alchemlyb>=2.0.0',
+        'pyyaml',
+        'seaborn',
+        'matplotlib',
+        'pyemma',
+    ],
     # platforms=['Linux',
     #            'Mac OS-X',
     #            'Unix',