From 73863c70b0883f662bdfc2ecb40a7f39199360d6 Mon Sep 17 00:00:00 2001
From: Christoph Knote <christoph.knote@med.uni-augsburg.de>
Date: Mon, 14 Mar 2022 14:40:51 +0100
Subject: [PATCH] Fix circular dependency issue
---
README.md | 30 ++++++++++++++--------------
pyproject.toml | 2 +-
src/boxmox/__init__.py | 2 +-
src/boxmox/experiment.py | 11 ++++------
tests/usage_examples/intermediate.py | 4 ++--
tests/usage_examples/run_tests.bash | 27 -------------------------
6 files changed, 23 insertions(+), 53 deletions(-)
delete mode 100644 tests/usage_examples/run_tests.bash
diff --git a/README.md b/README.md
index 0b16685..b7bce9c 100644
--- a/README.md
+++ b/README.md
@@ -3,27 +3,16 @@
``boxmox`` is the Python wrapper for the chemical box model BOXMOX (a standalone
C/Fortran executable).
-## Contributing
-
-We are looking forward to receiving your [new issue report](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox_pypackage/-/issues/new).
-
-If you'd like to contribute source code directly, please [create a fork](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox_pypackage),
-make your changes and then [submit a merge request](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox_pypackage/-/merge_requests/new) to the original project.
-
## Installation
### BOXMOX model needs to be installed
-The BOXMOX chemical box model needs to be installed and usable,
-and the KPP_HOME environment variable has to be set.
-
-You can download it from our website at https://mbees.med.uni-augsburg.de/boxmodeling.
+The BOXMOX chemical box model needs to be installed and the ``KPP_HOME`` environment variable has to be set. Download and instructions are our website at https://mbees.med.uni-augsburg.de/boxmodeling.
### Environment variable needs to be set
-Additionally, boxmox needs a path to write temporary model results
-to. This directory needs to be accessible and writeable by the
-user. Set it in your environment, e.g., through:
+Additionally, ``boxmox`` needs a path to write temporary model results
+to, given through the environment variable ``BOXMOX_WORK_PATH``. This directory needs to be accessible and writeable by the user. Set it in your environment, e.g., through:
```
export BOXMOX_WORK_PATH=/where/you/want/boxmox/to/write/stuff/to/
@@ -31,9 +20,20 @@ export BOXMOX_WORK_PATH=/where/you/want/boxmox/to/write/stuff/to/
Remember to close the shell and log in again for these changes to take effect.
+## Contributing
+
+We are looking forward to receiving your [new issue report](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox_pypackage/-/issues/new).
+
+If you'd like to contribute source code directly, please [create a fork](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox_pypackage),
+make your changes and then [submit a merge request](https://mbees.med.uni-augsburg.de/gitlab/mbees/boxmox_pypackage/-/merge_requests/new) to the original project.
+
# Changelog
-## 1.2.0 (2022-03-08)
+## 1.2.4 (2022-03-14)
+
+- Release on PyPI
+
+## 1.2.0 (2022-03-08) (not released)
- Updates to be compatible with BOXMOX 1.8
diff --git a/pyproject.toml b/pyproject.toml
index 836e917..fbbb29f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "boxmox"
-version = "1.2.2"
+version = "1.2.4"
description = "BOXMOX python interface"
license = "GPL-3.0-or-later"
authors = ["Christoph Knote <christoph.knote@med.uni-augsburg.de>"]
diff --git a/src/boxmox/__init__.py b/src/boxmox/__init__.py
index 30e3076..274bfc6 100644
--- a/src/boxmox/__init__.py
+++ b/src/boxmox/__init__.py
@@ -28,7 +28,7 @@ if not os.path.isdir(work_path):
else:
from .experiment import Experiment, ExperimentFromExample, ExperimentFromExistingRun, Namelist, examples, compiledMechs
-from .data import InputFile, InputFileOrig, InputFile17, Output, ConcentrationOutput, RatesOutput, AdjointOutput, JacobianOutput, HessianOutput
+from .data import InputFile, Output, ConcentrationOutput, RatesOutput, AdjointOutput, JacobianOutput, HessianOutput
from .fluxes import FluxParser
try:
diff --git a/src/boxmox/experiment.py b/src/boxmox/experiment.py
index 6fec027..b06347d 100644
--- a/src/boxmox/experiment.py
+++ b/src/boxmox/experiment.py
@@ -3,18 +3,15 @@ import subprocess as s
import threading
import shutil
import fnmatch
-import numpy as np
import datetime
import f90nml
-from . import _installation
-from . import InputFile, Output, ConcentrationOutput, RatesOutput, AdjointOutput, JacobianOutput, HessianOutput
+from .data import InputFile, Output, ConcentrationOutput, RatesOutput, AdjointOutput, JacobianOutput, HessianOutput
try:
- import matplotlib
from .plotter import ExperimentPlotter
except:
pass
-from . import FluxParser
+from .fluxes import FluxParser
workPath=os.environ['BOXMOX_WORK_PATH']
examplesPath=os.path.join(os.environ['KPP_HOME'], "case_studies")
@@ -205,7 +202,7 @@ class Experiment:
def _run(self, dumbOutput=False):
try:
- self.pid = s.Popen([ "./" + self.mechanism + ".exe" ], stdout=s.PIPE, bufsize=1, cwd=self.path)
+ self.pid = s.Popen([ "./" + self.mechanism + ".exe" ], stdout=s.PIPE, cwd=self.path)
self.pid.wait()
self._pp_run(dumbOutput=dumbOutput)
except Exception as e:
@@ -229,7 +226,7 @@ class Experiment:
for type in self.input:
with open( os.path.join(self.path, type + '.csv'), 'w') as f:
- self.input[type].write(f, version=self.version)
+ self.input[type].write(f)
pwd = os.getcwd()
os.chdir(self.path)
diff --git a/tests/usage_examples/intermediate.py b/tests/usage_examples/intermediate.py
index b889e31..5d10a46 100644
--- a/tests/usage_examples/intermediate.py
+++ b/tests/usage_examples/intermediate.py
@@ -3,8 +3,8 @@ import boxmox
import numpy as np
# evaluate differences in run with different NO2 initial conditions
-no2_ics = np.linspace(0.01, 0.3, 20)
-c2h4_ics = np.linspace(0.1, 2.000, 20)
+no2_ics = np.linspace(0.01, 0.3, 10)
+c2h4_ics = np.linspace(0.1, 2.000, 10)
X,Y = np.meshgrid(no2_ics, c2h4_ics)
Z = np.zeros_like(X)
diff --git a/tests/usage_examples/run_tests.bash b/tests/usage_examples/run_tests.bash
deleted file mode 100644
index c540750..0000000
--- a/tests/usage_examples/run_tests.bash
+++ /dev/null
@@ -1,27 +0,0 @@
-export KPP_HOME=/Users/lechriso/git/boxmox/boxmox/
-export PATH="$KPP_HOME/bin:$KPP_HOME/boxmox/bin:$PATH"
-export BOXMOX_WORK_PATH=/tmp/
-
-echo " - - - - "
-echo "PYTHON 2"
-echo
-echo "simple.py"
-echo
-python2 simple.py
-echo
-echo "intermediate.py"
-echo
-python2 intermediate.py
-echo
-
-echo " - - - - "
-echo "PYTHON 3"
-echo
-echo "simple.py"
-echo
-python3 simple.py
-echo
-echo "intermediate.py"
-echo
-python3 intermediate.py
-echo
--
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