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rwest merged 3 commits into from
May 26, 2023
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Improve conda installation instructions #2246

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587f194
Improve conda installation instructions: use repositories over Ananco…
mefuller Nov 27, 2021
a15b747
Fix sphinx formatting.
rwest May 24, 2023
353d769
Improve formatting of developer install instructions.
rwest May 24, 2023
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61 changes: 34 additions & 27 deletions documentation/source/users/rmg/installation/anacondaDeveloper.rst
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Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX
*******************************************************************************************

#. Download and install `Anaconda Individual Edition <https://www.anaconda.com/products/individual#Downloads>`.
#. Install the `conda` package manager, if you do not already have it (or Anaconda).
Select one of the following options:

The download will be a .sh file with a name like ``Anaconda3-2023.03-Linux-x86_64.sh``. Open a terminal in the same
directory as this file, and type the following to install Anaconda (replace the name of your .sh file below). ::
a. Users of Fedora Linux and Red Hat derivatives (RHEL, CentOS Stream) may install from the official repositories and EPEL, respectively, with the command ::

bash Anaconda3-2023.03-Linux-x86_64.sh
sudo dnf install conda

**When prompted to append Anaconda to your PATH, select or type Yes**. Install the Anaconda folder inside your home
directory (typically ``/home/YourUsername/`` in Linux and ``/Users/YourUsername`` in Mac). When prompted, you do not
need to install Microsoft VSCode (but feel free to if you are looking for a lightweight IDE).
b. All other users, download and install `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_.

Note that you should restart your terminal in order for the changes to take effect, as the installer will tell you.
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). ::

#. There are a few system-level dependencies which are required and should not be installed via Anaconda. These include
`Git <https://git-scm.com/>`_ for version control, `GNU Make <https://www.gnu.org/software/make/>`_,
and the C and C++ compilers from the `GNU Compiler Collection (GCC) <https://gcc.gnu.org/>`_ for compiling RMG.
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 <https://git-scm.com/>`_ for version control, `GNU Make <https://www.gnu.org/software/make/>`_, and the C and C++ compilers from the `GNU Compiler Collection (GCC) <https://gcc.gnu.org/>`_ for compiling RMG.

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.

On Ubuntu and Debian the package manager is ``apt`` ::

sudo apt install git gcc g++ make

On Fedora and Red Hat derivatives (RHEL 8+) the package manager is ``dnf`` ::

sudo dnf install git gcc gcc-c++ make
a. On Ubuntu and Debian the package manager is ``apt`` ::

sudo apt install git gcc g++ make

b. On Fedora and Red Hat derivatives (RHEL 8+) the package manager is ``dnf`` ::

sudo dnf install git gcc gcc-c++ make

Replace ``dnf`` with ``yum`` in the preceding for Red Hat 7 and lower.
c. For Red Hat 7 and lower, replace ``dnf`` with ``yum`` in the preceding.

On openSUSE the package manager is ``zypper``::
d. On openSUSE the package manager is ``zypper``::

sudo zypper install git gcc gcc-c++ make
sudo zypper install git gcc gcc-c++ make

On Manjaro or Arch Linux the package manager is ``pacman`` ::
e. On Manjaro or Arch Linux the package manager is ``pacman`` ::

sudo pacman -S git gcc make
sudo pacman -S git gcc make

For MacOS users, the above packages will not come preinstalled but 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 on
whether or not you would like to install the Command Line Tools.
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.
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24 changes: 18 additions & 6 deletions documentation/source/users/rmg/installation/anacondaUser.rst
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Expand Up @@ -5,22 +5,34 @@ Binary Installation Using Anaconda for Unix-Based Systems: Linux and Mac OSX
****************************************************************************


#. Download and install the `Anaconda Python Platform <https://www.anaconda.com/download/>`_ for Python 3.7.
#. Install the `conda` package manager, if you do not already have it (or Anaconda).
Select one of the following options:

The download will be a .sh file with a name like ``Anaconda3-2019.07-Linux-x86_64.sh``. Open a terminal in the same
directory as this file, and type the following to install Anaconda (replace the name of your .sh file below). ::
a. Users of Fedora Linux and Red Hat derivatives (RHEL, CentOS Stream) may install from the official repositories and EPEL, respectively, with the command ::

bash Anaconda3-2019.07-Linux-x86_64.sh
sudo dnf install conda

**When prompted to append Anaconda to your PATH, select or type Yes**. Install the Anaconda folder inside your home directory (typically ``/home/YourUsername/`` in Linux and ``/Users/YourUsername`` in Mac). When prompted, you do not need to install Microsoft VSCode (but feel free to if you are looking for a lightweight IDE).
b. All other users, download and install `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_.

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.

#. Install both RMG and the RMG-database binaries through the terminal. Dependencies will be installed automatically. It is safest to make a new conda environment for RMG and its dependencies. Type the following command into the terminal to create the new environment named 'rmg_env' containing the latest stable version of the RMG program and its database. ::

conda create -c defaults -c rmg -c rdkit -c cantera -c pytorch -c conda-forge --name rmg_env rmg rmgdatabase

Whenever you wish to use it you must first activate the environment::

source activate rmg_env
conda activate rmg_env

#. You may now run an RMG test job. Save the `Minimal Example Input File <https://raw.githubusercontent.com/ReactionMechanismGenerator/RMG-Py/master/examples/rmg/minimal/input.py>`_
to a local directory. Use the terminal to run your RMG job inside that folder using the following command ::
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