From 62c375c726b2c526af9b7fc661250e91e7e46423 Mon Sep 17 00:00:00 2001 From: Nicholas Tietje Date: Wed, 6 Mar 2024 16:59:12 -0500 Subject: [PATCH] removed libxrender1 from all installation commands except wsl/debian --- .../rmg/installation/anacondaDeveloper.rst | 666 +++++++++--------- 1 file changed, 333 insertions(+), 333 deletions(-) diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst index 7f861873a06..1f73756f134 100644 --- a/documentation/source/users/rmg/installation/anacondaDeveloper.rst +++ b/documentation/source/users/rmg/installation/anacondaDeveloper.rst @@ -1,333 +1,333 @@ -.. _anacondaDeveloper: - -******************************************************************************************* -Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX -******************************************************************************************* - -#. Install the `conda` package manager, if you do not already have it (or Anaconda). - Select one of the following options: - - a. Users of Fedora Linux and Red Hat derivatives (RHEL, CentOS Stream) may install from the official repositories and EPEL, respectively, with the command :: - - sudo dnf install conda - - b. All other users, download and install `Miniconda `_. - - The download will be a .sh file with a name like ``Miniconda3-latest-Linux-x86_64.sh``. - Open a terminal in the same directory as this file, and type the following to install Conda - (replace the name of your .sh file below). :: - - bash Miniconda3-latest-Linux-x86_64.sh - - **When prompted to append Anaconda to your PATH, select or type Yes**. - Install the Conda folder inside your home directory - (typically ``/home/YourUsername/`` in Linux and ``/Users/YourUsername`` in Mac). - - Note that you should reinitialize or restart your terminal in order for the changes to take effect, as the installer will tell you. - -#. There are a few system-level dependencies which are required and should not be installed via Conda. These include - `Git `_ for version control, `GNU Make `_, and the C and C++ compilers from the `GNU Compiler Collection (GCC) `_ for compiling RMG. For WSL users, `libxrender1 `_ may also need to be installed. - - For Linux users, you can check whether these are already installed by simply calling them via the command line, which - will let you know if they are missing. To install any missing packages, you should use the appropriate package manager - for your system. - - a. On Ubuntu and Debian the package manager is ``apt`` :: - - sudo apt install git gcc g++ make libxrender1 - - b. On Fedora and Red Hat derivatives (RHEL 8+) the package manager is ``dnf`` :: - - sudo dnf install git gcc gcc-c++ make libxrender1 - - c. For Red Hat 7 and lower, replace ``dnf`` with ``yum`` in the preceding. - - d. On openSUSE the package manager is ``zypper``:: - - sudo zypper install git gcc gcc-c++ make libxrender1 - - e. On Manjaro or Arch Linux the package manager is ``pacman`` :: - - sudo pacman -S git gcc make libxrender1 - - f. For MacOS users, the above packages can be easily obtained by installing the XCode Command Line Tools. - These are a set of packages relevant for software development which have been bundled together by Apple. - The easiest way to install this is to simply run one of the commands in the terminal, e.g. ``git``. - The terminal will then prompt you to install the Command Line Tools. - -#. Install the latest versions of RMG and RMG-database through cloning the source code via Git. Make sure to start in an - appropriate local directory where you want both RMG-Py and RMG-database folders to exist. - Github has deprecated password authentication from the command line, so it - is preferred to clone the repositories using ``ssh``:: - - git clone git@github.com:ReactionMechanismGenerator/RMG-Py.git - git clone git@github.com:ReactionMechanismGenerator/RMG-database.git - - It is still possible to clone the repositories using ``https`` if you are - unfamiliar with ``ssh``:: - - git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git - - For information on using ``ssh`` with GitHub see the `Connecting to GitHub with SSH `_ - -#. Switch the conda solver backend to speed up creation of the RMG environment :: - - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - -#. Navigate to the RMG-Py directory :: - - cd RMG-Py - -#. Apple silicon (M1+) users only: execute the following commands - **instead of** the following `conda env create -f environment.yml` step. - (This will tell conda that we want to the environment to use x86 - architecture rather than the native ARM64 architecture) :: - - conda create -n rmg_env - conda activate rmg_env - conda config --env --set subdir osx-64 - conda env update -f environment.yml - -#. Create the conda environment for RMG-Py:: - - conda env create -f environment.yml - - If either of these commands return an error due to being unable to find the ``conda`` command, - try to either close and reopen your terminal to refresh your environment variables - or type the following command. - - If on Linux or pre-Catalina MacOS (or if you have a bash shell):: - - source ~/.bashrc - - If on MacOS Catalina or later (or if you have a Z shell):: - - source ~/.zshrc - -#. Activate conda environment :: - - conda activate rmg_env - -#. Switch the conda solver to libmamba again, to accelerate any changes you might make to this conda environment in the future:: - - conda config --set solver libmamba - -#. Compile RMG-Py after activating the conda environment :: - - make - -#. Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any folder. - *This is important before the next step in which julia dependencies are installed.* - Also, add your RMG-Py folder to PATH to launch ``rmg.py`` from any folder. - - In general, these commands should be placed in the appropriate shell initialization file. - For Linux users using bash (the default on distributions mentioned here), these should be placed in ``~/.bashrc``. - For MacOS users using bash (default before MacOS Catalina), these should be placed in ``~/.bash_profile``, which you should create if it doesn't exist. - For MacOS users using zsh (default beginning in MacOS Catalina), these should be placed in ``~/.zshrc``. :: - - export PYTHONPATH=YourFolder/RMG-Py/:$PYTHONPATH - export PATH=YourFolder/RMG-Py/:$PATH - - NOTE: Make sure to change ``YourFolder`` to the path leading to the ``RMG-Py`` code. Not doing so will lead to an error stating that python cannot find the module ``rmgpy``. - - Be sure to either close and reopen your terminal to refresh your environment variables (``source ~/.bashrc`` or ``source ~/.zshrc``). - -#. Install and Link Julia dependencies: :: - - julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;' - - python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" - - -#. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). :: - - python-jl replace/with/path/to/rmg.py input.py - -You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules ` included in the RMG-Py package. - - -Debugging -========= - -If you wish to debug using the (very helpful) debugger in `VSCode `_, -here is an example launch configuration to put in your ``launch.json`` file, -which can be found in the ``.vscode`` folder. -You might have to edit them slightly to match your exact paths. Specifically, -you will need ``/opt/miniconda3/envs/rmg_env`` to point to where your conda environment is located. - -This configuration will allow you to debug the rms_constant_V example, running through -python-jl. :: - - { - "name": "Python: rmg.py rms_constant_V", - "type": "python", - "request": "launch", - "cwd": "${workspaceFolder}/", - "program": "rmg.py", - "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", - "args": [ - "examples/rmg/rms_constant_V/input.py", - ], - "console": "integratedTerminal", - "env": { - "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}", - "PYTHONPATH": "${workspaceFolder}/", - } - }, - -This configuration will allow you to debug a subset of the unit tests. -Open one of the many test files named ``*Test.py`` in ``test/rmgpy`` before you launch it:: - - { - "name": "Python: pytest Current File", - "type": "python", - "request": "launch", - "program": "/opt/miniconda3/envs/rmg_env/bin/pytest", - "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", - "args": [ - "--capture=no", - "--verbose", - "${file}" - ], - "console": "integratedTerminal", - "env": { - "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}", - "PYTHONPATH": "${workspaceFolder}/", - }, - }, - -This configuration will allow you to debug running all the database tests.:: - - { - "name": "Test RMG-database", - "type": "python", - "request": "launch", - "program": "/opt/miniconda3/envs/rmg_env/bin/pytest", - "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", - "args": [ - "--capture=no", - "--verbose", - "${workspaceFolder}/test/database/databaseTest.py" - ], - "console": "integratedTerminal", - "env": { - "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}", - "PYTHONPATH": "${workspaceFolder}/", - }, - }, - -This configuration will allow you to use the debugger breakpoints inside unit tests being run by the pytest framework:: - - { - "name": "Python: Debug Tests", - "type": "python", - "request": "launch", - "program": "${file}", - "purpose": ["debug-test"], - "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", - "console": "integratedTerminal", - "justMyCode": false, - "env": {"PYTEST_ADDOPTS": "--no-cov",} // without disabling coverage VS Code doesn't stop at breakpoints while debugging because pytest-cov is using the same technique to access the source code being run - } - -See more about testing in VSCode in the :ref:`Testing in VSCode ` section below. - -Test Suite -========== - -There are a number of basic tests you can run on the newly installed RMG. It is recommended to run them regularly to ensure the code and databases are behaving normally. -Make sure that the environment is active before running the tests: ``conda activate rmg_env``. - -#. **Unit test suite**: this will run all the unit tests in the ``rmgpy`` and ``arkane`` packages :: - - cd RMG-Py - make test - -#. **Functional test suite**: this will run all the functional tests in the ``rmgpy`` and ``arkane`` packages :: - - cd RMG-Py - make test-functional - - -#. **Database test suite**: this will run the database unit tests to ensure that groups, rate rules, and libraries are well-formed :: - - cd RMG-Py - make test-database - - -.. _vscode_testing: - -Testing in VSCode -================= - -Once you have the Python extension installed and a Python file open within the editor, -a test beaker icon will be displayed on the VS Code Activity bar. -The beaker icon is for the Test Explorer view. When opening the Test Explorer, -you will see a Configure Tests button if you don't have a test framework enabled. -Once you select Configure Tests, you will be prompted to select a test framework -(**select `pytest`**) -and a folder containing the tests -(**select `test`**). -To configure the rest of the settings, find the ``settings.json`` file in your ``.vscode`` folder. -You can use the following settings to configure the pytest framework:: - - "python.testing.pytestEnabled": true, - "python.testing.pytestPath": "python-jl -m pytest", - "python.testing.pytestArgs": [ - "-p", "julia.pytestplugin", - "--julia-compiled-modules=no", - "--ignore", "test/regression", - "-m", "not functional", - // "-n", "auto", // number of parallel processes, if you install pytest-xdist - "test" - ], - -To run the tests, you can click the Run All Tests button in the Test Explorer view. -Learn more at the `Python testing in Visual Studio Code `_ documentation. - -Given the time taken for Julia to compile things every time it launches, -you might find this to be painfully slow even for a simple test. -It may be possible to use ``--julia-sysimage=JULIA_SYSIMAGE`` instead of ``--julia-compiled-modules=no``, -or disable PyJulia entirely. -If you find a better way to do this, or clearer instructions, -please `update this section `_. - - -Running Examples -================ - -A number of basic examples can be run immediately. Additional example input files can be found in the ``RMG-Py/examples`` folder. Please read more on :ref:`Example Input Files ` in the documentation. - -#. **Minimal Example**: this will run an Ethane pyrolysis model. It should take less than a minute to complete. The results will be in the ``RMG-Py/testing/minimal`` folder:: - - cd RMG-Py - make eg1 - -#. **Hexadiene Example**: this will run a Hexadiene model with pressure dependence and QMTP. Note that you must have MOPAC installed for this to run. The results will be in the ``RMG-Py/testing/hexadiene`` folder:: - - cd RMG-Py - make eg2 - -#. **Liquid Phase Example**: this will run a liquid phase RMG model. The results will be in the ``RMG-Py/testing/liquid_phase`` folder :: - - cd RMG-Py - make eg3 - -#. **ThermoEstimator Example**: this will run the :ref:`Thermo Estimation Module ` on a few molecules. Note that you must have MOPAC installed for this to run completely. The results will be in the ``RMG-Py/testing/thermoEstimator`` folder :: - - cd RMG-Py - make eg4 - - -Building Documentation -====================== -To build the documentation (to test that you have it right before pushing to GitHub) you will need to install sphinx:: - - conda activate rmg_env - conda install sphinx - -Then you can build the documentation:: - - make documentation +.. _anacondaDeveloper: + +******************************************************************************************* +Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX +******************************************************************************************* + +#. Install the `conda` package manager, if you do not already have it (or Anaconda). + Select one of the following options: + + a. Users of Fedora Linux and Red Hat derivatives (RHEL, CentOS Stream) may install from the official repositories and EPEL, respectively, with the command :: + + sudo dnf install conda + + b. All other users, download and install `Miniconda `_. + + The download will be a .sh file with a name like ``Miniconda3-latest-Linux-x86_64.sh``. + Open a terminal in the same directory as this file, and type the following to install Conda + (replace the name of your .sh file below). :: + + bash Miniconda3-latest-Linux-x86_64.sh + + **When prompted to append Anaconda to your PATH, select or type Yes**. + Install the Conda folder inside your home directory + (typically ``/home/YourUsername/`` in Linux and ``/Users/YourUsername`` in Mac). + + Note that you should reinitialize or restart your terminal in order for the changes to take effect, as the installer will tell you. + +#. There are a few system-level dependencies which are required and should not be installed via Conda. These include + `Git `_ for version control, `GNU Make `_, and the C and C++ compilers from the `GNU Compiler Collection (GCC) `_ for compiling RMG. For WSL users, `libxrender1 `_ may also need to be installed. + + For Linux users, you can check whether these are already installed by simply calling them via the command line, which + will let you know if they are missing. To install any missing packages, you should use the appropriate package manager + for your system. + + a. On Ubuntu and Debian the package manager is ``apt`` :: + + sudo apt install git gcc g++ make libxrender1 + + b. On Fedora and Red Hat derivatives (RHEL 8+) the package manager is ``dnf`` :: + + sudo dnf install git gcc gcc-c++ make + + c. For Red Hat 7 and lower, replace ``dnf`` with ``yum`` in the preceding. + + d. On openSUSE the package manager is ``zypper``:: + + sudo zypper install git gcc gcc-c++ make + + e. On Manjaro or Arch Linux the package manager is ``pacman`` :: + + sudo pacman -S git gcc make + + f. For MacOS users, the above packages can be easily obtained by installing the XCode Command Line Tools. + These are a set of packages relevant for software development which have been bundled together by Apple. + The easiest way to install this is to simply run one of the commands in the terminal, e.g. ``git``. + The terminal will then prompt you to install the Command Line Tools. + +#. Install the latest versions of RMG and RMG-database through cloning the source code via Git. Make sure to start in an + appropriate local directory where you want both RMG-Py and RMG-database folders to exist. + Github has deprecated password authentication from the command line, so it + is preferred to clone the repositories using ``ssh``:: + + git clone git@github.com:ReactionMechanismGenerator/RMG-Py.git + git clone git@github.com:ReactionMechanismGenerator/RMG-database.git + + It is still possible to clone the repositories using ``https`` if you are + unfamiliar with ``ssh``:: + + git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git + git clone https://github.com/ReactionMechanismGenerator/RMG-database.git + + For information on using ``ssh`` with GitHub see the `Connecting to GitHub with SSH `_ + +#. Switch the conda solver backend to speed up creation of the RMG environment :: + + conda install -n base conda-libmamba-solver + conda config --set solver libmamba + +#. Navigate to the RMG-Py directory :: + + cd RMG-Py + +#. Apple silicon (M1+) users only: execute the following commands + **instead of** the following `conda env create -f environment.yml` step. + (This will tell conda that we want to the environment to use x86 + architecture rather than the native ARM64 architecture) :: + + conda create -n rmg_env + conda activate rmg_env + conda config --env --set subdir osx-64 + conda env update -f environment.yml + +#. Create the conda environment for RMG-Py:: + + conda env create -f environment.yml + + If either of these commands return an error due to being unable to find the ``conda`` command, + try to either close and reopen your terminal to refresh your environment variables + or type the following command. + + If on Linux or pre-Catalina MacOS (or if you have a bash shell):: + + source ~/.bashrc + + If on MacOS Catalina or later (or if you have a Z shell):: + + source ~/.zshrc + +#. Activate conda environment :: + + conda activate rmg_env + +#. Switch the conda solver to libmamba again, to accelerate any changes you might make to this conda environment in the future:: + + conda config --set solver libmamba + +#. Compile RMG-Py after activating the conda environment :: + + make + +#. Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any folder. + *This is important before the next step in which julia dependencies are installed.* + Also, add your RMG-Py folder to PATH to launch ``rmg.py`` from any folder. + + In general, these commands should be placed in the appropriate shell initialization file. + For Linux users using bash (the default on distributions mentioned here), these should be placed in ``~/.bashrc``. + For MacOS users using bash (default before MacOS Catalina), these should be placed in ``~/.bash_profile``, which you should create if it doesn't exist. + For MacOS users using zsh (default beginning in MacOS Catalina), these should be placed in ``~/.zshrc``. :: + + export PYTHONPATH=YourFolder/RMG-Py/:$PYTHONPATH + export PATH=YourFolder/RMG-Py/:$PATH + + NOTE: Make sure to change ``YourFolder`` to the path leading to the ``RMG-Py`` code. Not doing so will lead to an error stating that python cannot find the module ``rmgpy``. + + Be sure to either close and reopen your terminal to refresh your environment variables (``source ~/.bashrc`` or ``source ~/.zshrc``). + +#. Install and Link Julia dependencies: :: + + julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;' + + python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" + + +#. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). :: + + python-jl replace/with/path/to/rmg.py input.py + +You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules ` included in the RMG-Py package. + + +Debugging +========= + +If you wish to debug using the (very helpful) debugger in `VSCode `_, +here is an example launch configuration to put in your ``launch.json`` file, +which can be found in the ``.vscode`` folder. +You might have to edit them slightly to match your exact paths. Specifically, +you will need ``/opt/miniconda3/envs/rmg_env`` to point to where your conda environment is located. + +This configuration will allow you to debug the rms_constant_V example, running through +python-jl. :: + + { + "name": "Python: rmg.py rms_constant_V", + "type": "python", + "request": "launch", + "cwd": "${workspaceFolder}/", + "program": "rmg.py", + "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", + "args": [ + "examples/rmg/rms_constant_V/input.py", + ], + "console": "integratedTerminal", + "env": { + "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}", + "PYTHONPATH": "${workspaceFolder}/", + } + }, + +This configuration will allow you to debug a subset of the unit tests. +Open one of the many test files named ``*Test.py`` in ``test/rmgpy`` before you launch it:: + + { + "name": "Python: pytest Current File", + "type": "python", + "request": "launch", + "program": "/opt/miniconda3/envs/rmg_env/bin/pytest", + "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", + "args": [ + "--capture=no", + "--verbose", + "${file}" + ], + "console": "integratedTerminal", + "env": { + "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}", + "PYTHONPATH": "${workspaceFolder}/", + }, + }, + +This configuration will allow you to debug running all the database tests.:: + + { + "name": "Test RMG-database", + "type": "python", + "request": "launch", + "program": "/opt/miniconda3/envs/rmg_env/bin/pytest", + "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", + "args": [ + "--capture=no", + "--verbose", + "${workspaceFolder}/test/database/databaseTest.py" + ], + "console": "integratedTerminal", + "env": { + "PATH": "/opt/miniconda3/envs/rmg_env/bin:${env:PATH}", + "PYTHONPATH": "${workspaceFolder}/", + }, + }, + +This configuration will allow you to use the debugger breakpoints inside unit tests being run by the pytest framework:: + + { + "name": "Python: Debug Tests", + "type": "python", + "request": "launch", + "program": "${file}", + "purpose": ["debug-test"], + "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl", + "console": "integratedTerminal", + "justMyCode": false, + "env": {"PYTEST_ADDOPTS": "--no-cov",} // without disabling coverage VS Code doesn't stop at breakpoints while debugging because pytest-cov is using the same technique to access the source code being run + } + +See more about testing in VSCode in the :ref:`Testing in VSCode ` section below. + +Test Suite +========== + +There are a number of basic tests you can run on the newly installed RMG. It is recommended to run them regularly to ensure the code and databases are behaving normally. +Make sure that the environment is active before running the tests: ``conda activate rmg_env``. + +#. **Unit test suite**: this will run all the unit tests in the ``rmgpy`` and ``arkane`` packages :: + + cd RMG-Py + make test + +#. **Functional test suite**: this will run all the functional tests in the ``rmgpy`` and ``arkane`` packages :: + + cd RMG-Py + make test-functional + + +#. **Database test suite**: this will run the database unit tests to ensure that groups, rate rules, and libraries are well-formed :: + + cd RMG-Py + make test-database + + +.. _vscode_testing: + +Testing in VSCode +================= + +Once you have the Python extension installed and a Python file open within the editor, +a test beaker icon will be displayed on the VS Code Activity bar. +The beaker icon is for the Test Explorer view. When opening the Test Explorer, +you will see a Configure Tests button if you don't have a test framework enabled. +Once you select Configure Tests, you will be prompted to select a test framework +(**select `pytest`**) +and a folder containing the tests +(**select `test`**). +To configure the rest of the settings, find the ``settings.json`` file in your ``.vscode`` folder. +You can use the following settings to configure the pytest framework:: + + "python.testing.pytestEnabled": true, + "python.testing.pytestPath": "python-jl -m pytest", + "python.testing.pytestArgs": [ + "-p", "julia.pytestplugin", + "--julia-compiled-modules=no", + "--ignore", "test/regression", + "-m", "not functional", + // "-n", "auto", // number of parallel processes, if you install pytest-xdist + "test" + ], + +To run the tests, you can click the Run All Tests button in the Test Explorer view. +Learn more at the `Python testing in Visual Studio Code `_ documentation. + +Given the time taken for Julia to compile things every time it launches, +you might find this to be painfully slow even for a simple test. +It may be possible to use ``--julia-sysimage=JULIA_SYSIMAGE`` instead of ``--julia-compiled-modules=no``, +or disable PyJulia entirely. +If you find a better way to do this, or clearer instructions, +please `update this section `_. + + +Running Examples +================ + +A number of basic examples can be run immediately. Additional example input files can be found in the ``RMG-Py/examples`` folder. Please read more on :ref:`Example Input Files ` in the documentation. + +#. **Minimal Example**: this will run an Ethane pyrolysis model. It should take less than a minute to complete. The results will be in the ``RMG-Py/testing/minimal`` folder:: + + cd RMG-Py + make eg1 + +#. **Hexadiene Example**: this will run a Hexadiene model with pressure dependence and QMTP. Note that you must have MOPAC installed for this to run. The results will be in the ``RMG-Py/testing/hexadiene`` folder:: + + cd RMG-Py + make eg2 + +#. **Liquid Phase Example**: this will run a liquid phase RMG model. The results will be in the ``RMG-Py/testing/liquid_phase`` folder :: + + cd RMG-Py + make eg3 + +#. **ThermoEstimator Example**: this will run the :ref:`Thermo Estimation Module ` on a few molecules. Note that you must have MOPAC installed for this to run completely. The results will be in the ``RMG-Py/testing/thermoEstimator`` folder :: + + cd RMG-Py + make eg4 + + +Building Documentation +====================== +To build the documentation (to test that you have it right before pushing to GitHub) you will need to install sphinx:: + + conda activate rmg_env + conda install sphinx + +Then you can build the documentation:: + + make documentation