Merge pull request #5 from daavid00/developing

Updating to toml and documents

.github/workflows/CI.yml

@@ -36,7 +36,7 @@ jobs:
         sudo apt-get install mpi-default-bin
         sudo apt-get install libopm-simulators-bin
         
-    - name: Install test dependecies
+    - name: Install dependecies
       run: |
         pip install --upgrade pip setuptools wheel
         pip install -r dev-requirements.txt
@@ -47,9 +47,9 @@ 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

@@ -1,5 +1,5 @@
 [![Build Status](https://github.com/cssr-tools/pycopm/actions/workflows/CI.yml/badge.svg)](https://github.com/cssr-tools/pycopm/actions/workflows/CI.yml)
-<a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.8%20|%203.9%20|%203.10%20|%203.11%20|%203.12-blue.svg"></a>
+<a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.8%20to%203.12-blue.svg"></a>
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![DOI](https://zenodo.org/badge/815649176.svg)](https://zenodo.org/doi/10.5281/zenodo.12740838)
@@ -12,9 +12,9 @@ Creation of coarser models from given input decks.
 
 ## Installation
 You will first need to install
-* Flow (https://opm-project.org, Release 2024.04 or current master branches)
+* OPM Flow (https://opm-project.org, Release 2024.04 or current master branches)
 
-To install the _pycopm_ executable in an existing Python environment: 
+To install the _pycopm_ executable in an existing Python environment:
 
 ```bash
 pip install git+https://github.com/cssr-tools/pycopm.git
@@ -34,15 +34,13 @@ python3 -m venv vpycopm
 source vpycopm/bin/activate
 # Upgrade pip, setuptools, and wheel
 pip install --upgrade pip setuptools wheel
-# Install the pycopm package (in editable mode for contributions/modifications; otherwise, pip install .)
+# Install the pycopm package
 pip install -e .
 # For contributions/testing/linting, install the dev-requirements
 pip install -r dev-requirements.txt
 ``` 
 
-See the [_CI.yml_](https://github.com/OPM/pycopm/blob/main/.github/workflows/CI.yml) script for installation of OPM Flow (binary packages) and the pycopm package. If you are a Linux user (including the Windows subsystem for Linux), then you could try to build Flow from the master branches with mpi support, by running the script `./build_opm-flow_mpi.bash`, which in turn should build flow in the folder ./build/opm-simulators/bin/flow (you first need to install the [_OPM-Flow-prerequisites_](https://opm-project.org/?page_id=239)). 
-
-For macOS users, use at least a Python version of 3.10 (due to resdata), and run the `./build_opm-flow_macOS.bash` to build OPM Flow (the [_OPM-Flow-prerequisites_](https://opm-project.org/?page_id=239) can be installed via brew or macports).
+See the [_installation_](https://cssr-tools.github.io/pycopm/installation.html) for further details on building OPM Flow from the master branches in Linux, Windows, and macOS, as well as the opm Python package. 
 
 ## Running pycopm
 You can run _pycopm_ as a single command line:
@@ -52,4 +50,10 @@ pycopm -i some_input -o some_output_folder
 Run `pycopm --help` to see all possible command line argument options.
 
 ## Getting started
-See the [_examples_](https://cssr-tools.github.io/pycopm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pycopm/introduction.html).
+See the [_examples_](https://cssr-tools.github.io/pycopm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pycopm/introduction.html).
+
+## About pycopm
+The _pycopm_ package is being funded by the [_Center for Sustainable Subsurface Resources (CSSR)_](https://cssr.no) 
+[project no. 331841].
+This is work in progress.
+Contributions are more than welcome using the fork and pull request approach.

dev-requirements.txt

@@ -1,7 +1,7 @@
 black
-pylint
+numpydoc
 mypy
+pylint
 pytest-cov
 sphinx
-sphinx-rtd-theme
-pytest
+sphinx-rtd-theme

docs/_sources/index.rst.txt

@@ -7,6 +7,7 @@ Welcome to pycopm's documentation!
    :maxdepth: 4
 
    introduction
+   installation
    configuration_file
    examples
    api

docs/_sources/installation.rst.txt

@@ -0,0 +1,120 @@
+============
+Installation
+============
+
+Python package
+--------------
+
+To install the **pycopm** executable in an existing Python environment: 
+
+.. code-block:: bash
+
+    pip install git+https://github.com/cssr-tools/pycopm.git
+
+If you are interested in modifying the source code, then you can clone the repository and 
+install the Python requirements in a virtual environment with the following commands:
+
+.. code-block:: console
+
+    # Clone the repo
+    git clone https://github.com/cssr-tools/pycopm.git
+    # Get inside the folder
+    cd pycopm
+    # Create virtual environment
+    python3 -m venv vpycopm
+    # Activate virtual environment
+    source vpycopm/bin/activate
+    # Upgrade pip, setuptools, and wheel
+    pip install --upgrade pip setuptools wheel
+    # Install the pycopm package
+    pip install -e .
+    # For contributions/testing/linting, install the dev-requirements
+    pip install -r dev-requirements.txt
+
+OPM Flow
+--------
+You also need to install:
+
+* OPM Flow (https://opm-project.org, Release 2024.04 or current master branches)
+
+.. tip::
+
+    See the `CI.yml <https://github.com/cssr-tools/pycopm/blob/main/.github/workflows/CI.yml>`_ script 
+    for installation of OPM Flow (binary packages) and the pycopm package in Linux. 
+
+Source build in Linux/Windows
++++++++++++++++++++++++++++++
+If you are a Linux user (including the Windows subsystem for Linux), then you could try to build Flow (after installing the `prerequisites <https://opm-project.org/?page_id=239>`_) from the master branches with mpi support by running
+in the terminal the following lines (which in turn should build flow in the folder ./build/opm-simulators/bin/flow.): 
+
+.. code-block:: console
+
+    CURRENT_DIRECTORY="$PWD"
+
+    for repo in common grid models simulators
+    do
+        git clone https://github.com/OPM/opm-$repo.git
+    done
+
+    mkdir build
+
+    for repo in common grid models
+    do
+        mkdir build/opm-$repo
+        cd build/opm-$repo
+        cmake -DUSE_MPI=1 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
+        make -j5 opm$repo
+        cd ../..
+    done    
+
+    mkdir build/opm-simulators
+    cd build/opm-simulators
+    cmake -DUSE_MPI=1 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid;$CURRENT_DIRECTORY/build/opm-models" $CURRENT_DIRECTORY/opm-simulators
+    make -j5 flow
+    cd ../..
+
+
+.. tip::
+
+    You can create a .sh file (e.g., build_opm_mpi.sh), copy the previous lines, and run in the terminal **source build_opm_mpi.sh**  
+
+Source build in macOS
++++++++++++++++++++++
+For macOS, there are no available binary packages, so OPM Flow needs to be built from source, in addition to the dune libraries 
+(see the `prerequisites <https://opm-project.org/?page_id=239>`_, which can be installed using macports or brew). This can be achieved by the following lines:
+
+.. code-block:: console
+
+    CURRENT_DIRECTORY="$PWD"
+
+    for module in common geometry grid istl
+    do   git clone https://gitlab.dune-project.org/core/dune-$module.git --branch v2.9.1
+    done
+    for module in common geometry grid istl
+    do   ./dune-common/bin/dunecontrol --only=dune-$module cmake -DCMAKE_DISABLE_FIND_PACKAGE_MPI=1
+         ./dune-common/bin/dunecontrol --only=dune-$module make -j5
+    done
+
+    for repo in common grid models simulators
+    do
+        git clone https://github.com/OPM/opm-$repo.git
+    done
+
+    mkdir build
+
+    for repo in common grid models
+    do
+        mkdir build/opm-$repo
+        cd build/opm-$repo
+        cmake -DUSE_MPI=0 -DWITH_NDEBUG=1 -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$repo
+        cd ../..
+    done    
+
+    mkdir build/opm-simulators
+    cd build/opm-simulators
+    cmake -DUSE_MPI=0 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$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/build/opm-models" $CURRENT_DIRECTORY/opm-simulators
+    make -j5 flow
+    cd ../..
+
+In addition, use at least a Python version of 3.10 (due to the resdata Python package).

docs/_sources/introduction.rst.txt

@@ -42,17 +42,3 @@ where
 - \-y: Vector of y-coarsening (`` by default).
 - \-z: Vector of z-coarsening (`` by default).
 - \-e: Use `utf8` or `ISO-8859-1` encoding to read the deck (`ISO-8859-1` by default).
-
-Installation
-------------
-See the `Github page <https://github.com/cssr-tools/pycopm>`_.
-
-.. tip::
-    Check the `CI.yml <https://github.com/cssr-tools/pycopm/blob/main/.github/workflows/CI.yml>`_ file.
-
-Getting started
----------------
-See the :doc:`examples <./examples>`.
-
-.. tip::
-    Check the `tests <https://github.com/cssr-tools/pycopm/blob/main/tests>`_.

docs/_static/searchtools.js

@@ -178,7 +178,7 @@ const Search = {
 
   htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
+    for (const removalQuery of [".headerlink", "script", "style"]) {
       htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
     }
     if (anchor) {
@@ -328,13 +328,14 @@ const Search = {
     for (const [title, foundTitles] of Object.entries(allTitles)) {
       if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
-          let score = Math.round(100 * queryLower.length / title.length)
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
           normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
             null,
-            score,
+            score + boost,
             filenames[file],
           ]);
         }

docs/about.html

@@ -47,6 +47,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration file</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pycopm Python API</a></li>

docs/api.html

@@ -48,6 +48,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration file</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">pycopm Python API</a><ul>

docs/configuration_file.html

@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Examples" href="examples.html" />
-    <link rel="prev" title="Introduction" href="introduction.html" /> 
+    <link rel="prev" title="Installation" href="installation.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -48,6 +48,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Configuration file</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pycopm Python API</a></li>
@@ -224,7 +225,7 @@ <h1>Configuration file<a class="headerlink" href="#configuration-file" title="Li
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="introduction.html" class="btn btn-neutral float-left" title="Introduction" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="examples.html" class="btn btn-neutral float-right" title="Examples" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

docs/examples.html

@@ -48,6 +48,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration file</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Examples</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#via-configuration-files">Via configuration files</a><ul>

docs/genindex.html

@@ -45,6 +45,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration file</a></li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">pycopm Python API</a></li>