Merge pull request #128 from svalinn/pystell-path

Assume pystell is installed properly in Python environment
svalinn · Jul 16, 2024 · 837de9d · 837de9d
2 parents d4d8f20 + 09f9056
commit 837de9d
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Showing 9 changed files with 10 additions and 24 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM continuumio/miniconda3 as parastell-deps
+FROM continuumio/miniconda3 AS parastell-deps
 
 ENV TZ=America/Chicago
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
@@ -46,10 +46,4 @@ COPY ./environment.yml /environment.yml
 RUN conda env create -f environment.yml
 RUN echo "conda activate parastell_env" >> /opt/etc/bashrc
 
-WORKDIR /opt
-
-# Install PyStell-UW
-RUN git clone https://github.com/aaroncbader/pystell_uw.git
-ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw
-
 WORKDIR /
diff --git a/README.md b/README.md
@@ -44,15 +44,6 @@ While it is possible to use ParaStell with older versions of Cubit, additional s
 
 If you do not have a Coreform Cubit license, you may be able to get one through [Cubit Learn](https://coreform.com/products/coreform-cubit/free-meshing-software/) at no cost.
 
-### Install PyStell-UW
-Download and extract the PyStell-UW repository:
-
-```bash
-git clone https://github.com/aaroncbader/pystell_uw.git
-```
-
-or download the and extract the ZIP file from [PyStell-UW](https://github.com/aaroncbader/pystell_uw). Once extracted, add the repository directory to your `PYTHONPATH`.
-
 ## Install ParaStell
 Download and extract the ParaStell repository:
 

diff --git a/environment.yml b/environment.yml
@@ -17,4 +17,5 @@ dependencies:
   - pip:
       - netcdf4
       - pyyaml
-      - pytest
+      - pytest
+      - git+https://github.com/aaroncbader/pystell_uw.git
diff --git a/parastell/invessel_build.py b/parastell/invessel_build.py
@@ -7,7 +7,7 @@
 import cubit
 import cadquery as cq
 import cad_to_dagmc
-import src.pystell.read_vmec as read_vmec
+import pystell.read_vmec as read_vmec
 
 from . import log
 from .utils import (

diff --git a/parastell/nwl_utils.py b/parastell/nwl_utils.py
@@ -2,7 +2,7 @@
 import numpy as np
 from scipy.optimize import direct
 import openmc
-import src.pystell.read_vmec as read_vmec
+import pystell.read_vmec as read_vmec
 import matplotlib.pyplot as plt
 
 
@@ -349,4 +349,4 @@ def nwl_plot(
     nwl_mat = nwl_mat/area_array
     plot(nwl_mat, phi_pts, theta_pts, num_levels)
 
-    return nwl_mat, phi_pts, theta_pts, area_array
+    return nwl_mat, phi_pts, theta_pts, area_array
diff --git a/parastell/parastell.py b/parastell/parastell.py
@@ -4,7 +4,7 @@
 
 import cubit
 import numpy as np
-import src.pystell.read_vmec as read_vmec
+import pystell.read_vmec as read_vmec
 
 from . import log
 

diff --git a/parastell/source_mesh.py b/parastell/source_mesh.py
@@ -3,7 +3,7 @@
 
 import numpy as np
 from pymoab import core, types
-import src.pystell.read_vmec as read_vmec
+import pystell.read_vmec as read_vmec
 
 from . import log as log
 from .utils import read_yaml_config, filter_kwargs, m2cm

diff --git a/tests/test_invessel_build.py b/tests/test_invessel_build.py
@@ -7,7 +7,7 @@
 # dependencies correctly
 import parastell.invessel_build as ivb
 
-import src.pystell.read_vmec as read_vmec
+import pystell.read_vmec as read_vmec
 
 
 def remove_files():

diff --git a/tests/test_source_mesh.py b/tests/test_source_mesh.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import pytest
-import src.pystell.read_vmec as read_vmec
+import pystell.read_vmec as read_vmec
 
 import parastell.source_mesh as sm
-Original file line number
+Diff line change
@@ Expand Up / @@ -17,4 +17,5 @@ dependencies: @@
       - pip:
           - netcdf4
           - pyyaml
-          - pytest
+          - pytest
+          - git+https://github.com/aaroncbader/pystell_uw.git