Change installation instructions to specifically request v1.0.4 (#450)

* change installation instructions to specifically request v1.0.4 for installation (this version) * update index.rst year * add licence date change * add change in conf.py of year * year change in LICENSE.md * publish only to anaconda on releases * fix found typos in v1 documentation
POSYDON-code · Nov 27, 2024 · bb29288 · bb29288
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diff --git a/.github/workflows/publish-to-anaconda.yml b/.github/workflows/publish-to-anaconda.yml
@@ -1,9 +1,8 @@
 name: publish_conda
 
 on:
-  push:
-    branches:
-     - main
+  release:
+    types: [published]
 
 jobs:
   publish:

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2022, Tassos Fragos
+Copyright (c) 2024, Tassos Fragos
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "posydon" %}
-{% set version = "1.0.3" %}
+{% set version = "1.0.4" %}
 
 package:
   name: "{{ name|lower }}"

diff --git a/docs/about/licence.rst b/docs/about/licence.rst
@@ -6,7 +6,7 @@ Licence
 
 BSD 3-Clause License
 
-Copyright (c) 2022, Tassos Fragos
+Copyright (c) 2024, Tassos Fragos
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/docs/conf.py b/docs/conf.py
@@ -105,7 +105,7 @@
 
 # General information about the project.
 project = u'posydon'
-copyright = u'2022, Tassos Fragos'
+copyright = u'2024, Tassos Fragos'
 author = u'POSYDON Collaboration'
 
 # The version info for the project you're documenting, acts as replacement for

diff --git a/docs/index.rst b/docs/index.rst
@@ -73,7 +73,7 @@ Table of Contents
 License & Attribution
 ---------------------
 
-Copyright (c) 2022, Tassos Fragos
+Copyright (c) 2024, Tassos Fragos
 
 If you make use of POSYDON in your work, please cite our paper
 (`arXiv <https://arxiv.org/abs/2202.05892>`_,

diff --git a/docs/install/install.rst b/docs/install/install.rst
@@ -4,6 +4,15 @@
 Installation
 ############
 
+.. warning::
+
+    **POSYDON v1**
+
+    You are currently viewing the documentation for POSYDON v1.0.4. If you are
+    looking for the documentation of the latest version of POSYDON, please
+    visit the `latest documentation <https://posydon.org/POSYDON/>`_.
+
+
 The easiest way to start with POSYDON is to install it from Anaconda
 (Recommended way), and call an executable script that downloads the grid
 data automatically.
@@ -13,7 +22,7 @@ POSYDON manually through `github` (Manual Installation). Below we describe both
 ways.
 
 =========================================================
-Installing POSYDON v1.0.0 from Anaconda (Recommended way)
+Installing POSYDON v1.0.4 from Anaconda (Recommended way)
 =========================================================
 
 Installation
@@ -22,25 +31,25 @@ Installation
 We recommend using Anaconda and to install POSYDON in a virtual environment.
 We have created a package which can be accessed through conda-forge. On Linux,
 the new conda environment can be created (we have named our environment
-posydon-example, but you can choose any name), the conda-forge channel added,
+posydon_conda, but you can choose any name), the conda-forge channel added,
 and the required library installation can all be completed in one line using
 the terminal or command line:
 
 .. code-block::
 
-    conda create --name posydon-example -c posydon -c conda-forge posydon
+    conda create --name posydon_conda -c posydon -c conda-forge posydon=1.0.4
 
 On Mac (or if you have problems with the above command on Linux), these steps
 likely need to be separately run:
 
 .. code-block::
 
-    conda create -n posydon-conda python=3.7
-    conda activate posydon-conda
+    conda create -n posydon_conda python=3.7
+    conda activate posydon_conda
     conda config --add channels conda-forge
     conda config --add channels posydon
     conda config --set channel_priority false
-    conda install posydon
+    conda install posydon=1.0.4
 
 In case of OSX-ARM architectures, where many packages of Python 3.7 are not
 available, please use the following commands:
@@ -53,20 +62,20 @@ available, please use the following commands:
     conda config --add channels conda-forge
     conda config --add channels posydon
     conda install python=3.7
-    conda install posydon
+    conda install posydon=1.0.4
 
 Now, you can activate the environment with
 
 .. code-block::
 
-    conda activate posydon
+    conda activate posydon_conda
 
 
 Downloading the POSYDON data
 ----------------------------
 Because the data is large, ~10 GB, it must be downloaded
 with an explicit command. Export the path to where you want
-to clone the data, e.g. `/home/`, and download the data from
+to clone the data, e.g. ``/home/``, and download the data from
 ZENODO with the following commands
 
 .. code-block::
@@ -79,15 +88,15 @@ ZENODO with the following commands
 
 
 ==========================================================
-Installing POSYDON v.1.0 from GitHub (Manual Installation)
+Installing POSYDON v.1.0.4 from GitHub (Manual Installation)
 ==========================================================
 
 Creating a conda environment
 ----------------------------
 
 As above, we recommend using Anaconda to install POSYDON in a virtual
 environment. After creating the environment (you can choose any name, e.g.,
-`posydon`, or `posydon_env`) like this:
+``posydon``, or ``posydon_env``) like this:
 
 .. code-block::
 
@@ -102,11 +111,11 @@ proceed with the installation, you will need to activate the environment:
 
 Cloning POSYDON
 ---------------
-Clone the repository in a local directory, e.g. `/home/POSYDON/`, with
+Clone the repository in a local directory, e.g. ``/home/POSYDON/``, with
 
 .. code-block::
 
-    git clone https://github.com/POSYDON-code/POSYDON.git
+    git clone https://github.com/POSYDON-code/POSYDON.git --branch v1.0.4
 
 
 The directory will contain the following structure:
@@ -132,11 +141,13 @@ Export the path to the cloned POSYDON code (you can add this line to your
 Installing the package
 ~~~~~~~~~~~~~~~~~~~~~~
 From the cloned POSYDON directory execute the commands to install POSYDON and
-the `mpi4py` dependency (first make sure you are on the main branch!)
+the ``mpi4py`` dependency. 
+With the git cloning command above, you should have downloaded the v1.0.4 version of
+POSYDON.
 
 .. code-block::
 
-    git checkout main
+    cd $PATH_TO_POSYDON    
     pip install -e .
     conda install mpi4py
 

diff --git a/docs/visualization/plot1D/plot1D.rst b/docs/visualization/plot1D/plot1D.rst
@@ -1,7 +1,7 @@
 .. _plot1D:
 
 ##############################################
-1D plotting functionalities for POSYON GRIDS
+1D plotting functionalities for POSYDON GRIDS
 ##############################################
 
 

diff --git a/docs/visualization/plot2D/plot2D.rst b/docs/visualization/plot2D/plot2D.rst
@@ -1,7 +1,7 @@
 .. _plot2D:
 
 ##############################################
-2D plotting functionalities for POSYON GRIDS
+2D plotting functionalities for POSYDON GRIDS
 ##############################################
 
 Similar to our 1D plotting functions, we provide a series of 2D plotting

diff --git a/posydon/grids/post_processing.py b/posydon/grids/post_processing.py
@@ -47,8 +47,8 @@ def post_process_grid(grid, index=None, star_2_CO=True, MODEL=MODEL,
                       single_star=False, verbose=False):
     """Compute post processed quantitiy of any grid.
 
-    This function post process any supported grid and computes:
-    - Core collpase quantities for 5 prescritions given the fiducial POSYDON
+    This function post processes any supported grid and computes:
+    - Core collapse quantities for 5 prescriptions given the fiducial POSYDON
     assumption given in MODEL plus:
       A: direct collapse
       B: Fryer+12-rapid
@@ -58,13 +58,13 @@ def post_process_grid(grid, index=None, star_2_CO=True, MODEL=MODEL,
       for each prescrition we store the compact object state (WD/NS/BH),
       SN type (WD, ECSN, CCSN, PISN, PPISN), fallback mass fraction f_gb,
       compact object mass and spin.
-    - Core masses at he-depletion (used in Patton core collpase)
-    - Mass envelopes for common ennvelope step.
+    - Core masses at he-depletion (used in Patton core collapse)
+    - Mass envelopes for common envelope step.
 
     Parameters
     ----------
     grid : PSyGrid
-        MESA gri in PSyGrid format.
+        MESA grid in PSyGrid format.
     index : None, touple or int
         If None, loop over all indicies otherwise provide a range, e.g. [10,20]
         or a index, e.g. 42.
@@ -75,7 +75,7 @@ def post_process_grid(grid, index=None, star_2_CO=True, MODEL=MODEL,
     single_star : bool
         If `True` the PSyGrid contains single stars.
     verbose : bool
-        If `True` print on screen the results of each core collpase.
+        If `True` print the results of each core collapse on screen.
 
     Returns
     -------
@@ -84,7 +84,7 @@ def post_process_grid(grid, index=None, star_2_CO=True, MODEL=MODEL,
         processed values. This is used to ensure one to one mapping when
         appending the extra columns back to a grid.
     EXTRA_COLUMNS: dict
-        Dictionary containing all post processe quantities.
+        Dictionary containing all post processed quantities.
 
     """
     CORE_COLLAPSES = [['direct', ''], ['Fryer+12-rapid', ''],
@@ -227,7 +227,7 @@ def post_process_grid(grid, index=None, star_2_CO=True, MODEL=MODEL,
                 EXTRA_COLUMNS['S%s_center_other' % (j+1)].append(None)
 
         if not single_star:
-            # core collpase quantities
+            # core collapse quantities
             if interpolation_class in ['no_MT', 'stable_MT']:
                 if star_2_CO or TF1 == 'Primary has depleted central carbon':
                     star = binary.star_1
@@ -364,7 +364,7 @@ def add_post_processed_quantities(grid, MESA_dirs_EXTRA_COLUMNS, EXTRA_COLUMNS,
     """Append post processed quantity to a grid.
 
     This function appends the quantities computed in post_process_grid to any
-    grid. Note that this function ensure you can append the quantities only if
+    grid. Note that this function ensures you can append the quantities only if
     the grid follows the order of MESA_dirs_EXTRA_COLUMNS.
 
     Parameters
@@ -376,9 +376,9 @@ def add_post_processed_quantities(grid, MESA_dirs_EXTRA_COLUMNS, EXTRA_COLUMNS,
         processed values. This is used to ensure one to one mapping when
         appending the extra columns back to a grid.
     EXTRA_COLUMNS: dict
-        Dictionary containing all post processe quantities.
+        Dictionary containing all post processed quantities.
     verbose : bool
-        If `True` print on screen the results of each core collpase.
+        If `True` print the results of each core collapse on screen.
 
     """
     # check correspondance of EXTRA_COLUMNS with grid

diff --git a/posydon/grids/psygrid.py b/posydon/grids/psygrid.py
@@ -26,7 +26,7 @@
 
     NOTE: you can use a family of HDF5 files in case of file size restrictions.
     For example, using `mygrid.h5.%d` for the path when creating/loading grids,
-    implied that split files will be `mygrid.h5.0`, `mygrid.h5.1`, and so on.
+    implies that split files will be `mygrid.h5.0`, `mygrid.h5.1`, and so on.
     When overwriting the file, all the family is overwritten (effectively, the
     files are emptied to avoid remainder split files from previous operations.)
 
@@ -90,8 +90,8 @@
    to select the exact set of columns, provide them in a tuple instead of list.
 
 
-II. READING DATA FROM GRID
---------------------------
+II. READING DATA FROM A GRID
+----------------------------
 mygrid = PSyGrid("thegrid.h5")  # opens a stored grid
 
 # Indexing...
@@ -125,7 +125,7 @@
     for run in mygrid:
         print(run)
 
-c) Getting number of runs:
+c) Getting the number of runs:
 
     n_runs = len(psygrid)
 
@@ -159,8 +159,8 @@
 
     myrun.history1.star_mass + myrun.history1.star_mass
 
-loads the table two times! To reduce reading times, store in local variables
-all the tables that are going to be needed more than once:
+loads the table two times! To reduce reading times, store all the tables
+that are going to be needed more than once in local variables:
 
     myhistory1 = myrun.history1
     myhistory1.star_mass + myhistory1.star_mass

diff --git a/posydon/interpolation/IF_interpolation.py b/posydon/interpolation/IF_interpolation.py
@@ -1,4 +1,4 @@
-"""Module for performing initial-final inteprolation.
+"""Module for performing initial-final interpolation.
 
 We showcase the initial-final interpolator which plays a critical role in the
 evolving binary populations. To use the initial-final interpolator we first