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Add homepage itself to doctree
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@mcoughlin
mcoughlin committed Aug 22, 2023
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Expand Up @@ -18,7 +18,7 @@ For science users
If you are a science user and want to use NMMA for your analysis, you
can install NMMA using conda as follows:

.. code::
.. code::
conda create --name nmma_env python=3.10
conda install -c conda-forge nmma
Expand All @@ -30,12 +30,12 @@ If you have an issue, such as 'Solving environment: failed with initial frozen s
conda create --name nmma_env python=3.10
conda install mamba -c conda-forge
mamba install nmma -c conda-forge
If you are a developer or you want to build NMMA from source, please
refer to the developer section below.

.. note::
.. note::

The above may not work for arm64 Macs; see specifc instructions below. However, we are still working on getting NMMA to work on arm64 Macs.

Expand All @@ -52,20 +52,20 @@ Store.
On your Linux/WSL terminal, run the following commands to install
anaconda (replace 5.3.1 by the latest version):

.. code::
.. code::
wget https://repo.anaconda.com/archive/Anaconda3-5.3.1-Linux-x86_64.sh
bash Anaconda3-5.3.1-Linux-x86_64.sh
(For 32-bit installation, skip the ``\_64`` in both commands)

.. note::
.. note::

If you already have Anaconda3 installed, please make sure that it is updated to the latest version using `conda update --all`. Also check that you do not have multiple versions of Python installed in `usr/lib/` directory as it can cause version conflicts while installing dependencies.

Now do:

.. code::
.. code::
conda update --all
Expand All @@ -82,7 +82,7 @@ guide <./contributing.html>`__). Now, after forking, run the following
command to clone the repository into your currently directory (by
default, in your home directory):

.. code::
.. code::
git clone https://github.com/your_github_username/nmma
Expand All @@ -95,7 +95,7 @@ Change directory to the nmma folder:
Create a new environment using this command (environment name is
nmma_env in this case):

.. code::
.. code::
conda create --name nmma_env python=3.8
conda activate nmma_env
Expand All @@ -104,29 +104,29 @@ nmma_env in this case):

If this gives an error like: ``CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'``, then run:

.. code::
.. code::
source ~/anaconda3/etc/profile.d/conda.sh
then proceed with ``conda activate nmma_env``.

Get the latest pip version

.. code::
.. code::
pip install --upgrade pip
Check python and pip version like this:

.. code::
.. code::
python --version
pip --version
Python 3.8 and above and Pip 21.2 and above is ideal for this
installation. It is recommended to update these for your installation.

.. important::
.. important::

Python 3.11 is now supported by NMMA!

Expand All @@ -136,27 +136,27 @@ Install mpi4py:
conda install mpi4py
.. warning::
.. warning::

We discourage installing mpi4py with pip. The installation does not work properly due to issues with MPI header files, etc.

Install parallel-bilby:

.. code::
.. code::
conda install -c conda-forge parallel-bilby
.. note::
.. note::

Installing parallel-bilby takes quite some time. Please be patient. If you encounter any errors, please check the `parallel-bilby installation guide <https://lscsoft.docs.ligo.org/parallel_bilby/installation>`__ for more details.


.. note::
.. note::

For those installing on WSL with pip, you may encounter an issue with installing parallel-bilby due to a dependency on python-ligo-lw.
This can be resolved by installing gcc with the following command:

.. code::
.. code::
sudo apt-get install gcc
Expand All @@ -165,14 +165,14 @@ and attempting to install parallel-bilby again.
Install pymultinest (note this line may not work for arm64 Macs; see
specifc instructions below)

.. code::
.. code::
conda install -c conda-forge pymultinest
.. warning::
.. warning::

In case an error comes up during an NMMA analysis of the form:

.. code::
ERROR: Could not load MultiNest library "libmultinest.so"
Expand All @@ -188,12 +188,12 @@ given here:
Use the commands below to install the dependencies given in
requirements.txt file which are necessary for NMMA:

.. code::
.. code::
pip install -r requirements.txt
python setup.py install
.. note::
.. note::

There is an issue pip installing ``pyfftw`` on arm64 Mac systems; see the dedicated section below for a solution. If any package appeared to have an issue installing, you can first check by attempting to install it again using pip:

Expand All @@ -217,7 +217,7 @@ requirements.txt file which are necessary for NMMA:

``$ conda install -c conda-forge p-tqdm``

.. note::
.. note::

If everything has gone smoothly, all of these above mentioned "pip install something" commands will show that the requirements have already been satisfied. Otherwise, these will cover the dependencies if not covered by ``python setup.py install``. Also, if running ``python setup.py install`` shows something on the lines of "cannot cythonize without cython", do:

Expand All @@ -232,7 +232,7 @@ and redo ``python setup.py install``.
https://github.com/pyFFTW/pyFFTW/issues/349#issuecomment-1468638458).
To address, use ``Homebrew`` to run

.. code::
.. code::
brew install fftw
Expand All @@ -247,7 +247,7 @@ then add the following lines to your ``.zprofile`` or ``.bash_profile``:
Close and reopen your terminal and run

.. code::
.. code::
pip install pyfftw
Expand All @@ -260,7 +260,7 @@ complete the dependency installations.
and compile ``Multinest`` from the source. Within the ``nmma``
directory, run:

.. code::
.. code::
git clone https://github.com/JohannesBuchner/MultiNest
cd MultiNest/build
Expand All @@ -270,19 +270,19 @@ complete the dependency installations.
Next, add the following lines to your ``.zprofile`` or
``.bash_profile``:

.. code::
.. code::
export LD_LIBRARY_PATH=$HOME/nmma/MultiNest/lib:$LD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=$HOME/nmma/MultiNest/lib:$DYLD_LIBRARY_PATH
.. note::
.. note::

Modify these paths as appropriate for the location of your ``MultiNest`` installation. You can also combine the ``DYLD_LIBRARY_PATH`` lines for ``MultiNest`` and ``fftw`` (above) into a single line

3. There are also issues with ``tensorflow`` and arm64 Macs. If using
``tensorflow``, install it with the following commands:

.. code::
.. code::
pip install tensorflow-macos
pip install tensorflow-metal
Expand Down Expand Up @@ -312,7 +312,7 @@ Then the build process for the custom lalsuite can be started

.. code::
cd YOUR_CUSTOM_LALSUITE
cd YOUR_CUSTOM_LALSUITE
./00boot
./configure --prefix=YOUR_PREFIX --disable-all-lal --enable-swig-python --enable-lalsimulation --enable-lalframe
make; make install
Expand All @@ -327,14 +327,14 @@ It might happen that in the course of this some packages will be downgraded. You

Run the following commands:

.. code::
.. code::
ipython
import nmma
import nmma.em.analysis
import nmma.eos.create_injection
.. tip::
.. tip::

(Okay, last one!): if everything is ok, it's the end of the installation. But in case it shows that such-and-such modules are absent, feel free to install those modules by visiting their anaconda documentation and install
those with their given commands. In case modules like afterglowpy and dust_extinction are needed, don't hesitate to do it with pip (normally it shouldn't happen), but some modules may not install correctly in case of disturbance.
Expand All @@ -347,7 +347,7 @@ on, running setup.py does not typically finish without errors the first
time through. Experience has shown that in the vast majority of cases,
simply pinning versions such as:

.. code::
.. code::
pip install astropy==4.3.1
Expand All @@ -367,18 +367,18 @@ commonly, these are software like gfortran or mpi).
For example, on XSEDE’s Expanse cluster, one can start a terminal
session with:

.. code::
.. code::
module load sdsc
module load openmpi
and follow the instructions above.

.. note::
.. note::

If ``module load openmpi`` does not execute directly and it asks for dependencies, one can proceed with:

.. code::
.. code::
module load sdsc
module load cpu/0.15.4
Expand All @@ -393,13 +393,13 @@ On new Linux installations, we sometimes come across the warning:
If you do prefer to use ‘Times New Roman’ for all of your plotting
needs, you can install ``msttcorefonts`` with:

.. code::
.. code::
sudo apt install msttcorefonts -qq
After removing the matplotlib cache:

.. code::
.. code::
rm ~/.cache/matplotlib -rf
Expand All @@ -423,6 +423,7 @@ User Guide
.. toctree::
:maxdepth: 1

index
quick-start-guide
models
training
Expand Down

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