Merge pull request #6 from daavid00/dev

Small fixes to the readme and docs

.github/workflows/CI.yml

@@ -48,9 +48,9 @@ jobs:
         
     - name: Check code style and linting 
       run: |
-        black --check src/ tests/ setup.py
-        pylint src/ tests/ setup.py
-        mypy --ignore-missing-imports src/ tests/ setup.py
+        black --check src/ tests/
+        pylint src/ tests/
+        mypy --ignore-missing-imports src/ tests/
       
     - name: Run the tests
       run: |

README.md

@@ -41,7 +41,7 @@ pip install -e .
 pip install -r dev-requirements.txt
 ``` 
 
-See the [_installation_](https://cssr-tools.github.io/pyopmnearwell/examples.html) for further details on building OPM Flow from the master branches
+See the [_installation_](https://cssr-tools.github.io/pyopmnearwell/installation.html) for further details on building OPM Flow from the master branches
 in Linux, Windows, and macOS.
 
 ## Running pyopmnearwell
@@ -51,8 +51,8 @@ pyopmnearwell -i some_input.txt -o some_output_folder
 ```
 Run `pyopmnearwell --help` to see all possible command line 
 argument options. Inside the `some_input.txt` file you provide the path to the
-flow executable and simulation parameters. See the .txt files in the `examples/`,
-`tests/geometries/`, and `tests/models/` folders. 
+flow executable and simulation parameters. See the .txt files in the [_examples_](https://github.com/cssr-tools/pyopmnearwell/tree/main/examples),
+[_tests/geometries/_](https://github.com/cssr-tools/pyopmnearwell/tree/main/tests/geometries), and [_tests/models/_](https://github.com/cssr-tools/pyopmnearwell/tree/main/tests/models) folders. 
 
 ## Getting started
 See the [_examples_](https://cssr-tools.github.io/pyopmnearwell/examples.html) in the [_documentation_](https://cssr-tools.github.io/pyopmnearwell/introduction.html).

docs/_sources/installation.rst.txt

@@ -112,7 +112,7 @@ package (see the `prerequisites <https://opm-project.org/?page_id=239>`_, which
         mkdir build/opm-$repo
         cd build/opm-$repo
         cmake -DPYTHON_EXECUTABLE=$(which python) -DWITH_NDEBUG=1 -DUSE_MPI=0 -DOPM_ENABLE_PYTHON=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
-        make -j5 opm$repo
+        make -j5
         cd ../..
     done    
 
@@ -122,7 +122,7 @@ package (see the `prerequisites <https://opm-project.org/?page_id=239>`_, which
     make -j5 flow
     cd ../..
 
-    echo "export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/build/python" >> $CURRENT_DIRECTORY/vpyopmnearwell/bin/activate
+    echo "export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/python" >> $CURRENT_DIRECTORY/vpyopmnearwell/bin/activate
 
 
 This builds OPM Flow as well as the opm Python package, and it exports the required PYTHONPATH. Then after execution, deactivate and activate the Python virtual environment.

docs/_sources/introduction.rst.txt

@@ -35,14 +35,14 @@ The current implementation supports the following executable with the argument o
 
 where 
 
-- \-i, \-input: The base name of the :doc:`configuration file <./configuration_file>` ('input.txt' by default).
-- \-o, \-output: The base name of the :doc:`output folder <./output_folder>` ('output' by default).
-- \-p, \-plotting: Using the 'resdata' or 'opm' Python package to generate the figures ('resdata' by default, 'off' to skip the plotting).
-- \-c, \-compare: Compare the results from different output folders (write any name to actiate, '' by default).
-- \-g, \-generate: Run the whole framework ('all'), only run flow ('flow'), or only create plots ('plot') ('all' by default).
-- \-z, \-zoom: xlim in meters for the zoomed in plots (20 by default).
-- \-s, \-scale: Scale for the x axis in the figures: 'normal' or 'log' ('normal' by default).
-- \-m, \-model: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) ('co2store' by default).
+- \-i: The base name of the :doc:`configuration file <./configuration_file>` ('input.txt' by default).
+- \-o: The base name of the :doc:`output folder <./output_folder>` ('output' by default).
+- \-p: Using the 'resdata' or 'opm' Python package to generate the figures ('resdata' by default, 'off' to skip the plotting).
+- \-c: Compare the results from different output folders (write any name to actiate, '' by default).
+- \-g: Run the whole framework ('all'), only run flow ('flow'), or only create plots ('plot') ('all' by default).
+- \-z: xlim in meters for the zoomed in plots (20 by default).
+- \-s: Scale for the x axis in the figures: 'normal' or 'log' ('normal' by default).
+- \-m: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) ('co2store' by default).
 
 .. warning::
     The H2CH4 template in the h2store model folder is under development and it is based on an input deck available in 

docs/installation.html

@@ -191,7 +191,7 @@ <h3>Source build in macOS<a class="headerlink" href="#source-build-in-macos" tit
 <span class="go">    mkdir build/opm-$repo</span>
 <span class="go">    cd build/opm-$repo</span>
 <span class="go">    cmake -DPYTHON_EXECUTABLE=$(which python) -DWITH_NDEBUG=1 -DUSE_MPI=0 -DOPM_ENABLE_PYTHON=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=&quot;$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid&quot; $CURRENT_DIRECTORY/opm-$repo</span>
-<span class="go">    make -j5 opm$repo</span>
+<span class="go">    make -j5</span>
 <span class="go">    cd ../..</span>
 <span class="go">done</span>
 
@@ -201,7 +201,7 @@ <h3>Source build in macOS<a class="headerlink" href="#source-build-in-macos" tit
 <span class="go">make -j5 flow</span>
 <span class="go">cd ../..</span>
 
-<span class="go">echo &quot;export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/build/python&quot; &gt;&gt; $CURRENT_DIRECTORY/vpyopmnearwell/bin/activate</span>
+<span class="go">echo &quot;export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/python&quot; &gt;&gt; $CURRENT_DIRECTORY/vpyopmnearwell/bin/activate</span>
 </pre></div>
 </div>
 <p>This builds OPM Flow as well as the opm Python package, and it exports the required PYTHONPATH. Then after execution, deactivate and activate the Python virtual environment.</p>

docs/introduction.html

@@ -115,14 +115,14 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 </div>
 <p>where</p>
 <ul class="simple">
-<li><p>-i, -input: The base name of the <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> (‘input.txt’ by default).</p></li>
-<li><p>-o, -output: The base name of the <a class="reference internal" href="output_folder.html"><span class="doc">output folder</span></a> (‘output’ by default).</p></li>
-<li><p>-p, -plotting: Using the ‘resdata’ or ‘opm’ Python package to generate the figures (‘resdata’ by default, ‘off’ to skip the plotting).</p></li>
-<li><p>-c, -compare: Compare the results from different output folders (write any name to actiate, ‘’ by default).</p></li>
-<li><p>-g, -generate: Run the whole framework (‘all’), only run flow (‘flow’), or only create plots (‘plot’) (‘all’ by default).</p></li>
-<li><p>-z, -zoom: xlim in meters for the zoomed in plots (20 by default).</p></li>
-<li><p>-s, -scale: Scale for the x axis in the figures: ‘normal’ or ‘log’ (‘normal’ by default).</p></li>
-<li><p>-m, -model: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) (‘co2store’ by default).</p></li>
+<li><p>-i: The base name of the <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> (‘input.txt’ by default).</p></li>
+<li><p>-o: The base name of the <a class="reference internal" href="output_folder.html"><span class="doc">output folder</span></a> (‘output’ by default).</p></li>
+<li><p>-p: Using the ‘resdata’ or ‘opm’ Python package to generate the figures (‘resdata’ by default, ‘off’ to skip the plotting).</p></li>
+<li><p>-c: Compare the results from different output folders (write any name to actiate, ‘’ by default).</p></li>
+<li><p>-g: Run the whole framework (‘all’), only run flow (‘flow’), or only create plots (‘plot’) (‘all’ by default).</p></li>
+<li><p>-z: xlim in meters for the zoomed in plots (20 by default).</p></li>
+<li><p>-s: Scale for the x axis in the figures: ‘normal’ or ‘log’ (‘normal’ by default).</p></li>
+<li><p>-m: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) (‘co2store’ by default).</p></li>
 </ul>
 <div class="admonition warning">
 <p class="admonition-title">Warning</p>

docs/text/installation.rst

@@ -112,7 +112,7 @@ package (see the `prerequisites <https://opm-project.org/?page_id=239>`_, which
         mkdir build/opm-$repo
         cd build/opm-$repo
         cmake -DPYTHON_EXECUTABLE=$(which python) -DWITH_NDEBUG=1 -DUSE_MPI=0 -DOPM_ENABLE_PYTHON=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
-        make -j5 opm$repo
+        make -j5
         cd ../..
     done    
 
@@ -122,7 +122,7 @@ package (see the `prerequisites <https://opm-project.org/?page_id=239>`_, which
     make -j5 flow
     cd ../..
 
-    echo "export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/build/python" >> $CURRENT_DIRECTORY/vpyopmnearwell/bin/activate
+    echo "export PYTHONPATH=\$PYTHONPATH:$CURRENT_DIRECTORY/build/opm-common/python" >> $CURRENT_DIRECTORY/vpyopmnearwell/bin/activate
 
 
 This builds OPM Flow as well as the opm Python package, and it exports the required PYTHONPATH. Then after execution, deactivate and activate the Python virtual environment.

docs/text/introduction.rst

@@ -35,14 +35,14 @@ The current implementation supports the following executable with the argument o
 
 where 
 
-- \-i, \-input: The base name of the :doc:`configuration file <./configuration_file>` ('input.txt' by default).
-- \-o, \-output: The base name of the :doc:`output folder <./output_folder>` ('output' by default).
-- \-p, \-plotting: Using the 'resdata' or 'opm' Python package to generate the figures ('resdata' by default, 'off' to skip the plotting).
-- \-c, \-compare: Compare the results from different output folders (write any name to actiate, '' by default).
-- \-g, \-generate: Run the whole framework ('all'), only run flow ('flow'), or only create plots ('plot') ('all' by default).
-- \-z, \-zoom: xlim in meters for the zoomed in plots (20 by default).
-- \-s, \-scale: Scale for the x axis in the figures: 'normal' or 'log' ('normal' by default).
-- \-m, \-model: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) ('co2store' by default).
+- \-i: The base name of the :doc:`configuration file <./configuration_file>` ('input.txt' by default).
+- \-o: The base name of the :doc:`output folder <./output_folder>` ('output' by default).
+- \-p: Using the 'resdata' or 'opm' Python package to generate the figures ('resdata' by default, 'off' to skip the plotting).
+- \-c: Compare the results from different output folders (write any name to actiate, '' by default).
+- \-g: Run the whole framework ('all'), only run flow ('flow'), or only create plots ('plot') ('all' by default).
+- \-z: xlim in meters for the zoomed in plots (20 by default).
+- \-s: Scale for the x axis in the figures: 'normal' or 'log' ('normal' by default).
+- \-m: Simulated model (5th row in the configuration file). This is used for the plotting compare method (it gets overwritten by the configuration file) ('co2store' by default).
 
 .. warning::
     The H2CH4 template in the h2store model folder is under development and it is based on an input deck available in 

pyproject.toml

@@ -44,5 +44,5 @@ Homepage = "https://cssr-tools.github.io/pyopmnearwell"
 Repository = "https://github.com/cssr-tools/pyopmnearwell"
 
 [tool.setuptools]
-packages = ["pyopmnearwell"]
+packages.find.where = ["src"]
 platforms = ["all"]