Merge remote-tracking branch 'gyorilab/master' into depmap

Author: haohangyan

CONTRIBUTING.md

@@ -2,13 +2,13 @@ Git fork/PR workflow
 --------------------
 This repository uses the [forking model](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow)
 for collaboration. In this model,
-each developer forks the main (sorgerlab/indra) repository, pushes code
+each developer forks the main (gyorilab/indra) repository, pushes code
 only to branches in their own fork, and then submits pull requests to
-sorgerlab. After cloning your own fork of `indra`, you should add `sorgerlab`
+gyorilab. After cloning your own fork of `indra`, you should add `gyorilab`
 as a remote to be able to track the latest changes by doing
 
 ```
-git remote add sorgerlab https://github.com/sorgerlab/indra.git
+git remote add gyorilab https://github.com/gyorilab/indra.git
 ```
 
 When a PR is submitted from a branch, any further changes can be pushed
@@ -17,9 +17,9 @@ are automatically appended to the PR. Please always check the box on Github
 allowing the maintainers of the repo to make changes to the PR.
 
 In addition, as a convention, we only merge PRs whose branches are rebased
-on top of the latest sorgerlab/master. This means that instead of merging
-sorgerlab/master into your own branch to resolve conflicts, you should always
-rebase on top of sorgerlab/master and force push your branches if
+on top of the latest gyorilab/master. This means that instead of merging
+gyorilab/master into your own branch to resolve conflicts, you should always
+rebase on top of gyorilab/master and force push your branches if
 needed (you can do this even if a PR from that branch is already open).
 Consistent with this convention, in general, you should not use `git pull`
 to update your local fork. Rather, use `git fetch --all`,
@@ -32,7 +32,7 @@ some commits before merging.
 
 Pull requests
 -------------
-Always submit PRs via the sorgerlab repository.
+Always submit PRs via the gyorilab repository.
 Give your PR a concise and clear title that describes without excessive detail
 what the PR does. You should give more details in the description, pointing
 out the important changes made and any additional remarks that are relevant.

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2014, INDRA Developers.
+Copyright (c) 2025, INDRA Developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,17 +1,17 @@
 # INDRA
 
 [![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
-[![Build](https://github.com/sorgerlab/indra/workflows/Tests/badge.svg)](https://github.com/sorgerlab/indra/actions)
+[![Build](https://github.com/gyorilab/indra/workflows/Tests/badge.svg)](https://github.com/gyorilab/indra/actions)
 [![Documentation](https://readthedocs.org/projects/indra/badge/?version=latest)](https://indra.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/indra.svg)](https://badge.fury.io/py/indra)
 [![Python 3](https://img.shields.io/pypi/pyversions/indra.svg)](https://www.python.org/downloads/release/python-357/)
 
-<img align="left" src="https://raw.githubusercontent.com/sorgerlab/indra/master/doc/indra_logo.png" width="300" height="224" />
+<img align="left" src="https://raw.githubusercontent.com/gyorilab/indra/master/doc/indra_logo.png" width="300" height="224" />
 
 INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated
 model assembly system, originally developed for molecular systems biology and
 then generalized to other domains (see [INDRA
-World](https://github.com/indralab/indra_world)). INDRA draws on natural
+World](https://github.com/gyorilab/indra_world)). INDRA draws on natural
 language processing systems and structured databases to collect mechanistic and
 causal assertions, represents them in a standardized form (INDRA Statements),
 and assembles them into various modeling formalisms including causal graphs and
@@ -265,7 +265,7 @@ full compatibility is currently only tested with 3.8-3.10.
 The preferred way to install INDRA is by pointing pip to the source repository
 as
 
-    $ pip install git+https://github.com/sorgerlab/indra.git
+    $ pip install git+https://github.com/gyorilab/indra.git
 
 Releases of INDRA are also available on
 [PyPI](https://pip.pypa.io/en/latest/installing/), you can install the latest

doc/conf.py

@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.23'
+version = '1.24'
 # The full version, including alpha/beta/rc tags.
-release = '1.23.0'
+release = '1.24.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/installation.rst

@@ -32,14 +32,14 @@ To install directly from Github, do:
 
 .. code-block:: bash
 
-    pip install git+https://github.com/sorgerlab/indra.git
+    pip install git+https://github.com/gyorilab/indra.git
 
 Or first clone the repository to a local folder and use pip to install
 INDRA from there locally:
 
 .. code-block:: bash
 
-    git clone https://github.com/sorgerlab/indra.git
+    git clone https://github.com/gyorilab/indra.git
     cd indra
     pip install .
 
@@ -50,7 +50,7 @@ as a system-wide package.
 
 .. code-block:: bash
 
-    git clone https://github.com/sorgerlab/indra.git
+    git clone https://github.com/gyorilab/indra.git
 
 To be able to use INDRA this way, you need
 to make sure that all its requirements are installed. To be able to

doc/tutorials/gene_network.rst

@@ -139,7 +139,7 @@ You can also read more about the pre-assembly
 process in the
 `preassembly module documentation <../modules/preassembler/index.html>`_ and
 in the `GitHub documentation
-<https://github.com/sorgerlab/indra#internal-knowledge-assembly>`_
+<https://github.com/gyorilab/indra#internal-knowledge-assembly>`_
 
 Assemble the statements into a network model
 --------------------------------------------
@@ -212,6 +212,6 @@ and look into the `natural language modeling tutorial <nl_modeling.html>`_
 which uses PySB models.
 
 Read more about all assembly output formats in the `README <https://github
-.com/sorgerlab/indra#output-model-assemblers>`_ and in the `module
+.com/gyorilab/indra#output-model-assemblers>`_ and in the `module
 references <https://indra.readthedocs.io/en/latest/modules/assemblers/index
 .html>`_.

docker/Dockerfile

@@ -34,7 +34,7 @@ RUN python3 -m venv $VENV_PATH
 ENV PATH="$VENV_PATH/bin:$PATH"
 
 # Install INDRA and dependencies
-RUN git clone https://github.com/sorgerlab/indra.git && \
+RUN git clone https://github.com/gyorilab/indra.git && \
     cd indra && \
     git checkout $BUILD_BRANCH && \
     git branch && \

indra/__init__.py

@@ -2,7 +2,7 @@
 import logging
 import os
 import sys
-__version__ = '1.23.0'
+__version__ = '1.24.0'
 
 __all__ = ['assemblers', 'belief', 'databases', 'explanation', 'literature',
            'mechlinker', 'preassembler', 'sources', 'tools', 'util']

indra/assemblers/pysb/bmi_wrapper.py

@@ -379,7 +379,7 @@ def make_repository_component(self):
         component.append(au)
 
         hu = etree.Element('help_url')
-        hu.text = 'http://github.com/sorgerlab/indra'
+        hu.text = 'http://github.com/gyorilab/indra'
         component.append(hu)
 
         for tag in ('cfg_template', 'time_step_type', 'time_units',

indra/databases/identifiers.py

@@ -37,6 +37,7 @@
     'OMIM', 'LSPCI', 'UPLOC', 'BFO', 'CCLE', 'CLO', 'GENBANK', 'CALOHA',
     'DRUGBANK.SALT', 'SMILES', 'NIHREPORTER.PROJECT', 'GOOGLE.PATENT', 'SPINE',
     'VO', 'EMAPA', 'INO', 'CIDO', 'OAE', 'OHPI', 'PHIPO', 'NLM', 'ISNI',
+    'RXNORM', 'HEMONC', 'DRUGSATFDA.NDA'
 }
 
 # These are reverse mappings from identifiers.org namespaces to INDRA