Start bundling into a package

.gitignore

@@ -42,3 +42,6 @@ examples/**/*.pdf
 
 # Ignore matrices
 *.mat
+
+# Ignore pip folder
+*egg-info/*
\ No newline at end of file

.gitlab-ci.yml

@@ -26,7 +26,7 @@ build:environment:
   - docker build --cache-from $CI_REGISTRY_IMAGE:latest --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE:latest .
   # - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA # no need
   - docker push $CI_REGISTRY_IMAGE:latest
-  when: manual # skips 15min, but has to be done manually if Dockerfile changes
+  only: tags # skips 15min, but has to be done manually if Dockerfile changes
 
 build:doc:
   stage: build
@@ -48,12 +48,22 @@ build:doc:
       - ${DOCS_DIRECTORY}/_build/latex/
     expire_in: 6 month
 
+build:app:
+  stage: build
+  image:
+    name: $CI_REGISTRY_IMAGE:latest
+    entrypoint: [""]
+  script:
+    - pip install .
+
 # **************************************************************************** #
 # test
 # **************************************************************************** #
 
 .test: # dot means "hidden", acts as base class
   stage: test
+  dependencies:
+    - build:app
   image:
     name: $CI_REGISTRY_IMAGE:latest # use prebuilt image in Gitlab's registry
     entrypoint: [""] # == Repo. Has to be done if Dockerfile has own entrypoint

Dockerfile

@@ -37,6 +37,10 @@ RUN \
 COPY requirements.txt /tmp/
 RUN pip install --requirement /tmp/requirements.txt
 
+# Install the fenicsR13 package (puts it into the PATH)
+COPY . /tmp/
+RUN pip install --editable /tmp/.
+
 # Replace default FEniCS Docker WELCOME screen with custom WELCOME screen
 COPY WELCOME .
 RUN echo "Built: $(date)" >> WELCOME
\ No newline at end of file

MANIFEST.in

+include README.rst
\ No newline at end of file

README.rst

@@ -77,7 +77,7 @@ To run a simulation execute the solver main program ``fenicsR13.py`` (which is l
 .. code-block:: bash
 
     # Run program with given input file:
-    python3 ../../src/fenicsR13.py input.yml
+    fenicsR13 input.yml
 
 
 Output files will be written to a folder which is named after the ``output_folder`` keyword of the ``input.yml``. For immediate inspection the output folder contains simple visualizations in PDF files for each of the fields (temperature, pressure,...).
@@ -103,7 +103,7 @@ We provide a simple example of a flow through a finite-length channel in 2D.
     # Create mesh:
     ./create_mesh.sh
     # Run program with given input file:
-    python3 ../../src/fenicsR13.py input.yml
+    fenicsR13 input.yml
 
 In the output folder the results can be post-processed to demonstrate the `Knudsen paradox`_ in a simple table.
 
@@ -130,7 +130,7 @@ We can test the convergence of the R13 discretization on a simple double-cylindr
     # Meshes are already in Git:
     ls ../mesh
     # Run program with given input file:
-    python3 ../../src/fenicsR13.py inputs/r13_1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml
+    fenicsR13 inputs/r13_1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml
     # Go to folder with simulation results (=casename in input.yml)
     cd r13_1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab
     # Open errors:
@@ -150,7 +150,7 @@ FEniCS allows simple parallelization using MPI
 
     # Parallel execution ("-u" to flash stdout)
     # Usage: mpirun -n <numberOfProcesses> <serialCommand>
-    # E.g.: mpirun -n 4 python3 -u ../../src/fenicsR13.py input.yml
+    # E.g.: mpirun -n 4 fenicsR13 input.yml
 
 Building the Docker Image Locally
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -207,7 +207,7 @@ Developer Tips
 
     .. code-block:: bash
 
-        htop -p `{ python3 ../../src/fenicsR13.py inputs/1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml > /dev/null & } && echo $!`
+        htop -p `{ fenicsR13 inputs/1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml > /dev/null & } && echo $!`
 
 - Use doctest with ``python3 -m doctest -v src/meshes.py``
 - Run ``pydocstyle`` once in a while
@@ -317,7 +317,7 @@ Further Installation Tips
 **Interactive Jupyter Notebooks with Microsoft's Visual Studio Code**
 
 This is may be a convenient solution.
-Run a file with ``%run ../../src/fenicsr13.py``
+Run a file with ``%run ../../fenicsr13/fenicsr13.py``
 
 **X11 Window Forwarding on OSX**
 

examples/channel_flow/create_mesh.sh

 #!/bin/bash
-python3 ../../src/geoToH5.py channel.geo channel5.h5 "-setnumber p 5"
\ No newline at end of file
+geoToH5 channel.geo channel5.h5 "-setnumber p 5"
\ No newline at end of file

examples/knudsen_pump/create_mesh.sh

 #!/bin/bash
-python3 ../../src/geoToH5.py knudsen_pump.geo knudsen_pump4.h5 "-setnumber p 4"
\ No newline at end of file
+geoToH5 knudsen_pump.geo knudsen_pump4.h5 "-setnumber p 4"
\ No newline at end of file

examples/lid_driven_cavity/create_mesh.sh

 #!/bin/bash
-python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
\ No newline at end of file
+geoToH5 lid.geo lid5.h5 "-setnumber p 5"
\ No newline at end of file

examples/test_examples.py

@@ -14,7 +14,7 @@ class TestExamples(object):
     All tests are compared against reference errors.
     """
 
-    solver_path = "../../src/fenicsR13.py"
+    solver_path = "fenicsR13"
 
     def run_solver(self, inputfile, working_dir_):
         """
@@ -23,7 +23,7 @@ class TestExamples(object):
         Test fails if subprocess return Exception or error.
         """
         subprocess.check_call([
-            "python3", self.solver_path, inputfile
+            self.solver_path, inputfile
         ], cwd=working_dir_)
 
     # @pytest.fixture(scope="module", autouse=True)

fenicsR13/__init__.py

+# pylint: disable=invalid-name,missing-module-docstring
+
+from .fenicsR13 import *
+from .geoToH5 import *
+from .input import *
+from .meshes import *
+from .postprocessor import *
+from .solver import *
+from .tensoroperations import *

src/fenicsR13.py → fenicsR13/fenicsR13.py

@@ -15,10 +15,10 @@ import sys
 import gc
 import dolfin as df
 
-import meshes
-from input import Input
-from solver import Solver
-from postprocessor import Postprocessor
+from fenicsR13.meshes import H5Mesh
+from fenicsR13.input import Input
+from fenicsR13.solver import Solver
+from fenicsR13.postprocessor import Postprocessor
 
 def print_information():
     r"""
@@ -63,10 +63,13 @@ def main():
 
     .. code-block:: bash
 
+        # Install fenicsR13
+        pip install .
+
         # Usage: <path_to_program> <input_file>
         # Goto case folder:
         cd tests/r13
-        python3 ../../src/fenicsR13.py inputs/ \
+        fenicsR13 inputs/ \
           r13_1_coeffs_nosources_norot_inflow_p1p1p1p1p1_stab.yml
 
     """
@@ -108,7 +111,7 @@ def main():
 
             mesh_name = mesh_names[p]
 
-            current_mesh = meshes.H5Mesh(mesh_name)
+            current_mesh = H5Mesh(mesh_name)
             solver = Solver(params, current_mesh, p)
 
             solver.assemble()

src/geoToH5.py → fenicsR13/geoToH5.py

@@ -5,13 +5,19 @@
 """
 Converter from geo-format to a mesh in h5-format.
 
+Installation:
+
+.. coe-block:: bash
+
+    pip install .
+
 Usage:
 
 .. code-block:: bash
 
     Usage: python3 <path_to_geoToH5.py> <geo_file> <h5_file> \
             [<gmsh cli arguments>]
-    E.g.: python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
+    E.g.: geoToH5 lid.geo lid5.h5 "-setnumber p 5"
 """
 
 import os
@@ -29,7 +35,7 @@ def geo_to_h5():
     if not 3 <= len(sys.argv) <= 4:
         print("""
 Usage: python3 <path_to_geoToH5.py> <geo_file> <h5_file> [<gmsh cli arguments>]
-E.g.: python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
+E.g.: geoToH5 lid.geo lid5.h5 "-setnumber p 5"
         """)
         return
 
@@ -68,10 +74,3 @@ E.g.: python3 ../../src/geoToH5.py lid.geo lid5.h5 "-setnumber p 5"
     file.write(mesh, "/mesh")
     file.write(subdomains, "/subdomains")
     file.write(boundaries, "/boundaries")
-
-def main():
-    "Execute the converter."
-    geo_to_h5()
-
-if __name__ == '__main__':
-    main()

src/solver.py → fenicsR13/solver.py

@@ -12,7 +12,7 @@ import time as time_module
 import dolfin as df
 import ufl
 import numpy as np
-import tensoroperations as to
+import fenicsR13.tensoroperations as to
 
 
 class Solver:
@@ -47,8 +47,8 @@ class Solver:
     Example
     -------
     >>> # Example usage:
-    >>> from input import Input
-    >>> from meshes import H5Mesh
+    >>> from fenicsR13.input import Input
+    >>> from fenicsR13.meshes import H5Mesh
     >>> params = Input(
     ...     "tests/heat/inputs/heat_01_coeffs_p1p1_stab.yml"
     ... ) # doctest: +ELLIPSIS
@@ -1131,8 +1131,8 @@ class Solver:
         >>> print(rhs.get_local())
         [ 0.25  0.5   0.25]
         >>> # Assign LHS to solver
-        >>> from input import Input
-        >>> from meshes import H5Mesh
+        >>> from fenicsR13.input import Input
+        >>> from fenicsR13.meshes import H5Mesh
         >>> params = Input(
         ...     "tests/heat/inputs/heat_01_coeffs_p1p1_stab.yml"
         ... ) # doctest: +ELLIPSIS

pytest.ini

 [pytest]
-testpaths = src examples/test_examples.py tests
+testpaths = fenicsR13 examples/test_examples.py tests
 addopts = --doctest-modules --cov --cov-report=term --cov-report=html

setup.py

+"Setup file"
+
+from setuptools import setup
+
+def readme(): # pylint: disable=missing-function-docstring
+    with open('README.rst') as file:
+        return file.read()
+
+setup(
+    name="fenicsR13",
+    version="1.0",
+    description="FEniCS (FEM) Solver for Non.-Eq.-Gases Based on R13 Equations",
+    long_description=readme(),
+    url="https://git.rwth-aachen.de/lamBOO/fenicsR13",
+    author="Lambert Theisen, Manuel Torrilhon",
+    author_email="lambert.theisen@rwth-aachen.de, mt@mathcces.rwth-aachen.de",
+    license="None",
+    packages=["fenicsR13"],
+    zip_safe=False,
+    entry_points={
+        "console_scripts": [
+            "fenicsR13=fenicsR13.fenicsR13:main",
+            "geoToH5=fenicsR13.geoToH5:geo_to_h5"
+        ],
+    }
+)

tests/heat/test_heat_convergence.py

@@ -15,7 +15,7 @@ class TestHeatConvergence(object):
     """
 
     working_dir = "tests/heat"
-    solver_path = "../../src/fenicsR13.py"
+    solver_path = "fenicsR13"
 
     def run_solver(self, inputfile):
         """
@@ -24,7 +24,7 @@ class TestHeatConvergence(object):
         Test fails if subprocess return Exception or error.
         """
         subprocess.check_call([
-            "python3", self.solver_path, inputfile
+            self.solver_path, inputfile
         ], cwd=self.working_dir)
 
     def compare_errors(self, errorsfile, ref_errorsfile):