Pytest fixes, Path fix and faster pip install (#47)

* Version numbers are strings not floats

* Change trigger to on pull_request

* We moved away from requirements.txt sometime ago.

* It would be nice to install pytest

* Fixed triple calls from setup.py

Fixes #41

* Added Path for the output_dir

No longer string / string

.github/workflows/pytest.yml

@@ -1,7 +1,7 @@
 name: Run pytest
 
 on:
-  push:
+  pull_request:
     branches:
       - main
       - develop  # Add the 'develop' branch here
@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.10  # Specify the Python version you need
+        python-version: "3.10"  # Specify the Python version you need
 
     - name: Install gfortran
       run: |
@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt  # Replace with the path to your requirements file
+        pip install pytest
     
     - name: Install package in editable mode
       run: |

setup.py

@@ -1,4 +1,3 @@
-import setuptools  # this is the "magic" import
 import subprocess
 import sys
 
@@ -9,17 +8,20 @@
 
 #make clean every time slows things but is needed because users will mostly install after changing networks
 #and a make never seems to full update the new network
-cwd = os.getcwd()
-os.chdir('src/fortran_src/')
-result = subprocess.call('make clean', shell=True)
-# if result != 0:
-#     exit(1)
-result = subprocess.call('make python', shell=True)
-if result != 0:
-    exit(1)
-os.chdir(cwd)
-
-wrap_file = glob("src/fortran_src/uclchemwrap*.so")[0]
-move(wrap_file, "src/uclchem/uclchemwrap.so")
+# print(f"STAGE: {sys.argv[1]}, full command: {sys.argv}")
+if sys.argv[1] in ("editable_wheel"):
+    cwd = os.getcwd()
+    os.chdir('src/fortran_src/')
+    _ = subprocess.call('make clean', shell=True)
+    result = subprocess.call('make python', shell=True)
+    if result != 0:
+        exit(1)
+    os.chdir(cwd)
 
+    wrap_file = glob("src/fortran_src/uclchemwrap*.so")[0]
+    move(wrap_file, "src/uclchem/uclchemwrap.so")
+elif sys.argv[1] in ("bdist_wheel"):
+    raise RuntimeError("Cannot install UCLCHEM in the site packages, use `pip install -e .`")
+else:
+    pass
 setup()

src/uclchem/makerates/io_functions.py

@@ -215,6 +215,7 @@ def write_outputs(network: Network, output_dir: str = None) -> None:
         output_dir = Path("../src/uclchem")
         fortran_src_dir = Path("../src/fortran_src")
     else:
+        output_dir = Path(output_dir)
         fortran_src_dir = Path(output_dir)
 
     # Create the species file