easylink 0.1.12__tar.gz → 0.1.14__tar.gz

{easylink-0.1.12 → easylink-0.1.14}/.github/CODEOWNERS

@@ -1,2 +1,2 @@
 # default owners
-* @aflaxman @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier @zmbc
+* @aflaxman @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier @tylerdy @zmbc

{easylink-0.1.12 → easylink-0.1.14}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**0.1.14 - 5/1/25**
+
+ - Add support for EmbarrassinglyParallelSteps to accept sections (i.e. non-leaf steps)
+
+**0.1.13 - 4/21/25**
+
+ - remove graphviz from doc build install
+
 **0.1.12 - 4/1/25**
 
  - Propagate embarrassingly parallel splitters and aggregators to leaf steps

easylink-0.1.14/CONTRIBUTING.rst

@@ -0,0 +1,12 @@
+============
+Contributing
+============
+
+To run or develop easylink tests or documentation, you can install easylink with the ``[dev]`` extra::
+
+    $ git clone git@github.com:ihmeuw/easylink.git # or git clone https://github.com/ihmeuw/easylink.git
+    $ cd easylink
+    $ pip install -e .[dev]
+
+.. todo::
+    Show how to run the tests and build the documentation

{easylink-0.1.12 → easylink-0.1.14}/Makefile

@@ -14,6 +14,9 @@ PACKAGE_NAME = easylink
 include $(MAKE_INCLUDES)/base.mk
 include $(MAKE_INCLUDES)/test.mk
 
+install: ENV_REQS?=dev
 install:
-	conda install -y python-graphviz
-	$(MAKE) -f $(MAKE_INCLUDES)/base.mk install
+# Don't install Graphviz for docs. This could break if we add doctests which require graphviz!
+# Note that installing the python package graphviz doesn't actually require the graphviz system package.
+	$(if $(filter-out docs,${ENV_REQS}),conda install -y python-graphviz,)
+	$(MAKE) -f $(MAKE_INCLUDES)/base.mk install ENV_REQS=${ENV_REQS}

{easylink-0.1.12 → easylink-0.1.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easylink
-Version: 0.1.12
+Version: 0.1.14
 Summary: Research repository for the EasyLink ER ecosystem project.
 Home-page: https://github.com/ihmeuw/easylink
 Author: The EasyLink developers
@@ -19,11 +19,14 @@ Requires-Dist: pyarrow
 Requires-Dist: snakemake>=8.0.0
 Requires-Dist: snakemake-interface-executor-plugins<9.0.0
 Requires-Dist: snakemake-executor-plugin-slurm
+Requires-Dist: pandas-stubs
+Requires-Dist: pyarrow-stubs
 Provides-Extra: docs
 Requires-Dist: sphinx<8.2.0; extra == "docs"
 Requires-Dist: sphinx-rtd-theme; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
 Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
 Requires-Dist: typing_extensions; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
@@ -34,6 +37,7 @@ Requires-Dist: sphinx<8.2.0; extra == "dev"
 Requires-Dist: sphinx-rtd-theme; extra == "dev"
 Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
 Requires-Dist: sphinx-click; extra == "dev"
+Requires-Dist: sphinx-autobuild; extra == "dev"
 Requires-Dist: typing_extensions; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
@@ -71,28 +75,32 @@ Installation
 
 There are a few things to install in order to use this package:
 
-- Install singularity. If this is not already installed on your system, you will 
-  likely need to request it from your system admin. 
-  Refer to https://docs.sylabs.io/guides/4.1/admin-guide/installation.html
+- Install singularity. 
 
+  You may need to request it from your system admin. 
+  Refer to https://docs.sylabs.io/guides/4.1/admin-guide/installation.html. 
+  You can check if you already have singularity installed by running the command ``singularity --version``. For an
+  existing installation, your singularity version number is printed.
 
-- Install graphviz via:
+- Install conda. 
+  
+  We recommend `miniforge <https://github.com/conda-forge/miniforge>`_. You can check if you already
+  have conda installed by running the command ``conda --version``. For an existing installation, a version 
+  will be displayed.
 
-  .. code-block:: console
-
-    $ conda install graphviz
-
-- Install EasyLink.
+- Install easylink, python and graphviz in a conda environment.
 
   Option 1 - Install from PyPI with pip::
 
+    $ conda create --name easylink -c conda-forge python=3.12 graphviz 'gcc<14' -y
+    $ conda activate easylink
     $ pip install easylink
 
   Option 2 - Build from source with pip::
-
-    $ git clone git@github.com:ihmeuw/easylink.git  # or git clone https://github.com/ihmeuw/easylink.git
-    $ cd easylink
-    $ pip install .
+    
+    $ conda create --name easylink -c conda-forge python=3.12 graphviz 'gcc<14' -y
+    $ conda activate easylink
+    $ pip install git+https://github.com/ihmeuw/easylink.git
 
 .. _end_installation:
 

easylink-0.1.14/README.rst

@@ -0,0 +1,53 @@
+========
+EasyLink
+========
+
+EasyLink is a framework that allows users to build and run highly configurable
+entity resolution (ER) pipelines.
+
+.. _python_support:
+
+**Supported Python versions: 3.11, 3.12**
+
+.. _end_python_support:
+
+Installation
+============
+
+.. _installation:
+
+There are a few things to install in order to use this package:
+
+- Install singularity. 
+
+  You may need to request it from your system admin. 
+  Refer to https://docs.sylabs.io/guides/4.1/admin-guide/installation.html. 
+  You can check if you already have singularity installed by running the command ``singularity --version``. For an
+  existing installation, your singularity version number is printed.
+
+- Install conda. 
+  
+  We recommend `miniforge <https://github.com/conda-forge/miniforge>`_. You can check if you already
+  have conda installed by running the command ``conda --version``. For an existing installation, a version 
+  will be displayed.
+
+- Install easylink, python and graphviz in a conda environment.
+
+  Option 1 - Install from PyPI with pip::
+
+    $ conda create --name easylink -c conda-forge python=3.12 graphviz 'gcc<14' -y
+    $ conda activate easylink
+    $ pip install easylink
+
+  Option 2 - Build from source with pip::
+    
+    $ conda create --name easylink -c conda-forge python=3.12 graphviz 'gcc<14' -y
+    $ conda activate easylink
+    $ pip install git+https://github.com/ihmeuw/easylink.git
+
+.. _end_installation:
+
+Documentation
+=============
+
+You can view documentation at https://easylink.readthedocs.io/en/latest/