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Assume pystell is installed properly in Python environment #128

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merged 7 commits into from
Jul 16, 2024
Merged

Assume pystell is installed properly in Python environment #128

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885582e
Assume pystell is installed properly in Python environment
paulromano Jul 10, 2024
ce99dc6
Temporarily use PYTHONPATH for pystell in Dockerfile
paulromano Jul 10, 2024
44de981
Modify PYTHONPATH in ci.yml
paulromano Jul 10, 2024
b1dd42d
Fix Dinstall of pystell in Dockerfile
paulromano Jul 11, 2024
d6c4144
add pystell to pip dependencies in environment.yml
Edgar-21 Jul 12, 2024
1ddc648
update readme to reflect that pystell is in environment.yml
Edgar-21 Jul 12, 2024
09f9056
Merge pull request #131 from svalinn/add_pystell_to_environment
paulromano Jul 14, 2024
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8 changes: 1 addition & 7 deletions Dockerfile
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@@ -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
Expand Down Expand Up @@ -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 /
9 changes: 0 additions & 9 deletions README.md
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Expand Up @@ -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:

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3 changes: 2 additions & 1 deletion environment.yml
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Expand Up @@ -17,4 +17,5 @@ dependencies:
- pip:
- netcdf4
- pyyaml
- pytest
- pytest
- git+https://github.com/aaroncbader/pystell_uw.git
2 changes: 1 addition & 1 deletion parastell/invessel_build.py
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Expand Up @@ -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 (
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4 changes: 2 additions & 2 deletions parastell/nwl_utils.py
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Expand Up @@ -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


Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion parastell/parastell.py
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion parastell/source_mesh.py
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/test_invessel_build.py
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Expand Up @@ -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():
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2 changes: 1 addition & 1 deletion tests/test_source_mesh.py
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Expand Up @@ -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

Expand Down