Merge pull request #133 from GENESIS-EFRC/dev

Add carbonate correction, ability to turn off enumeration parallelization, minor bug fixes, new numba
materialsproject · May 26, 2022 · f85a827 · f85a827
2 parents 56a9d3d + 7c6b045
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diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-reaction-network Copyright (c) 2021, The Regents of the University of
+reaction-network Copyright (c) 2022, The Regents of the University of
 California, through Lawrence Berkeley National Laboratory (subject
 to receipt of any required approvals from the U.S. Dept. of Energy).
 All rights reserved.

diff --git a/README.md b/README.md
@@ -8,22 +8,19 @@ pathways in solid-state materials synthesis using combinatorial and graph-theort
 
 # Installation directions
 
-The rxn-network package has several dependencies, most of which can be installed
-through PyPI. However, graph-tool must be installed through a more customized method;
-please see https://graph-tool.skewed.de/ for more details. We recommend the
-following installation procedure which creates a new conda environment with Python 3.9,
-activates it, and then installs graph-tool through conda-forge.
+This package can be easily installed using pip:
 
 ```properties
-conda create -n gt python=3.9
-conda activate gt
-conda install -c conda-forge graph-tool
+pip install reaction-network
 ```
 
-Reaction network can then simply be installed via pip:
+:warning: While this will take care of most dependencies, if you are using any of the network-based features (i.e. within `rxn_network.network`), then `graph-tool` must be installed. Unfortunately, this cannot
+be installed through pip; please see https://graph-tool.skewed.de/ for more details. :warning:
+
+We recommend the following installation procedure which installs graph-tool through conda-forge.
 
 ```properties
-pip install reaction-network
+conda install -c conda-forge graph-tool
 ```
 
 ## For developers: 

diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -1,9 +1,5 @@
 # Changelog
 
-## [v6.0.0](https://github.com/GENESIS-EFRC/reaction-network/tree/v6.0.0) (2022-03-31)
-
-[Full Changelog](https://github.com/GENESIS-EFRC/reaction-network/compare/v5.0.0...v6.0.0)
-
 ## [v5.0.0](https://github.com/GENESIS-EFRC/reaction-network/tree/v5.0.0) (2022-03-31)
 
 [Full Changelog](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.3.0...v5.0.0)

diff --git a/docs/index.md b/docs/index.md
@@ -1,4 +1,4 @@
-# ![Reaction Network](images/logo.png)
+# ![Reaction Network](docs/images/logo.png)
 
 [![Pytest Status](https://github.com/GENESIS-EFRC/reaction-network/workflows/testing/badge.svg)](https://github.com/GENESIS-EFRC/reaction-network/actions?query=workflow%3Atesting)
 [![Code Coverage](https://codecov.io/gh/GENESIS-EFRC/reaction-network/branch/main/graph/badge.svg)](https://codecov.io/gh/GENESIS-EFRC/reaction-network)
@@ -8,19 +8,23 @@ pathways in solid-state materials synthesis using combinatorial and graph-theort
 
 # Installation directions
 
-The rxn-network package has several dependencies, most of which can be installed
-through PyPI. However, graph-tool must be installed through a more customized method;
-please see https://graph-tool.skewed.de/ for more details. We recommend the
-following installation procedure which creates a new conda environment with Python 3.9,
-activates it, and then installs graph-tool through conda-forge.
+This package can be easily installed using pip:
+
+```properties
+pip install reaction-network
+```
+
+:warning: While this will take care of most dependencies, if you are using any of the network-based features (i.e. within `rxn_network.network`), then `graph-tool` must be installed. Unfortunately, this cannot
+be installed through pip; please see https://graph-tool.skewed.de/ for more details. :warning:
+
+We recommend the following installation procedure which installs graph-tool through conda-forge.
 
 ```properties
-conda create -n gt python=3.9
-conda activate gt
 conda install -c conda-forge graph-tool
 ```
 
-To install an editable version of the rxn-network code, simply download (clone) the
+## For developers: 
+To install an editable version of the rxn-network code, simply clone the
 code from this repository, navigate to its directory, and then run the
 following command to install the requirements:
 
@@ -29,6 +33,9 @@ pip install -r requirements.txt
 pip install -e .
 ```
 
+Note that this only works if the repository is cloned from GitHub, such that it contains
+the proper metadata.
+
 # Tutorial notebooks
 
 The `notebooks` folder contains two (2) demonstration notebooks: 

diff --git a/docs/reference/builders/retrosynthesis.md b/docs/reference/builders/retrosynthesis.md
@@ -0,0 +1 @@
+::: rxn_network.builders.retrosynthesis
diff --git a/docs/reference/costs/competition.md b/docs/reference/costs/competition.md
@@ -0,0 +1 @@
+::: rxn_network.costs.competition
diff --git a/docs/reference/costs/competitiveness.md b/docs/reference/costs/competitiveness.md
diff --git a/docs/reference/entries/corrections.md b/docs/reference/entries/corrections.md
@@ -0,0 +1 @@
+::: rxn_network.entries.corrections
diff --git a/docs/reference/entries/freed.md b/docs/reference/entries/freed.md
@@ -0,0 +1 @@
+::: rxn_network.entries.freed
diff --git a/docs/reference/utils/models.md b/docs/reference/utils/models.md
@@ -0,0 +1 @@
+::: rxn_network.utils.models
diff --git a/docs/reference/utils/ray.md b/docs/reference/utils/ray.md
@@ -0,0 +1 @@
+::: rxn_network.utils.ray
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,6 +1,6 @@
-site_name: Reaction Network Documentation
-site_description: Documentation for rxn_network
-copyright: Built by The GENESIS EFRC
+site_name: Reaction-network documentation
+site_description: Documentation for the reaction-network package
+copyright: Built by Matthew McDermott (GENESIS-EFRC)
 
 nav:
   - Home: index.md
@@ -10,6 +10,8 @@ nav:
         - Network: 
             - Network: network.ipynb
   - Reference:
+      - Builders:
+          Retrosynthesis: reference/builders/retrosynthesis.md
       - Core:
           Calculator: reference/core/calculator.md
           Cost Function: reference/core/cost_function.md
@@ -20,13 +22,15 @@ nav:
           Solver: reference/core/solver.md
       - Costs:
           Calculators: reference/costs/calculators.md
-          Competitiveness: reference/costs/competitiveness.md
+          Competition: reference/costs/competition.md
           Softplus: reference/costs/softplus.md
       - Data: reference/data/data.md
       - Entries:
           Barin: reference/entries/barin.md
+          Corrections: reference/entries/corrections.md
           Entry Set: reference/entries/entry_set.md
           Experimental: reference/entries/experimental.md
+          Freed: reference/entries/freed.md
           Gibbs: reference/entries/gibbs.md
           Nist: reference/entries/nist.md
       - Enumerators:
@@ -64,6 +68,8 @@ nav:
       - Utils:
           Database: reference/utils/database.md
           Funcs: reference/utils/funcs.md
+          Models: reference/utils/models.md
+          Ray: reference/utils/ray.md
   - CHANGELOG: CHANGELOG.md
 
 repo_url: https://github.com/GENESIS-EFRC/reaction-network/