Fix circular dependency issue

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
 

pyproject.toml

 [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>"]

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:

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)

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)

tests/usage_examples/run_tests.bash

-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