Merge pull request #371 from mabruzzo/rename-gracklepy

The *Great Renaming:* `gracklepy` edition

Author: mabruzzo

.circleci/config.yml

@@ -36,7 +36,7 @@ commands:
           command: |
             source $BASH_ENV
             # libtool-bin is a requirement of the classic build-system
-            # castxml is a requirement of the pygrackle test-suite
+            # castxml is a requirement of the gracklepy test-suite
             sudo apt install -y libtool-bin castxml
             python3 -m venv $HOME/venv
             source $HOME/venv/bin/activate
@@ -53,7 +53,7 @@ commands:
             source $BASH_ENV
             source $HOME/venv/bin/activate
             cd src/python
-            flake8 pygrackle examples tests
+            flake8 gracklepy examples tests
 
   install-grackle:
     description: "Install the core Grackle Library & Pygrackle."
@@ -120,15 +120,15 @@ commands:
               Grackle_DIR=${PWD}/build pip install -v -e .
             fi
 
-  install-standalone-pygrackle:
-    description: "Install pygrackle without explicitly building the grackle library."
+  install-standalone-gracklepy:
+    description: "Install gracklepy without explicitly building the grackle library."
     parameters:
       tag:
         type: string
         default: $CIRCLE_BRANCH
     steps:
       - run:
-          name: "Install pygrackle."
+          name: "Install gracklepy."
           command: |
             source $HOME/venv/bin/activate
             git checkout << parameters.tag >>
@@ -154,8 +154,8 @@ commands:
             source $BASH_ENV  # sets up YT_DATA_DIR, env variable
             ./scripts/ci/fetch_test_data.py
 
-  run-pygrackle-tests:
-    description: "Run the pytest test-suite. This suite includes a mix of general tests and pygrackle-specific tests."
+  run-gracklepy-tests:
+    description: "Run the pytest test-suite. This suite includes a mix of general tests and gracklepy-specific tests."
     parameters:
       omp:
         type: enum
@@ -164,7 +164,7 @@ commands:
       build_kind:
         type: enum
         default: 'classic'
-        enum: ['classic', 'cmake', 'standalone-pygrackle']
+        enum: ['classic', 'cmake', 'standalone-gracklepy']
       generate:
         type: enum
         default: 'true'
@@ -179,7 +179,7 @@ commands:
             # actually execute the tests
             if [[ '<< parameters.build_kind >>' == 'classic' &&
                   '<< parameters.omp >>' == 'true' ]]; then
-              echo "ERROR: pygrackle tests can't be run in this configuration"
+              echo "ERROR: gracklepy tests can't be run in this configuration"
               exit 1
 
             else
@@ -194,8 +194,8 @@ commands:
               fi
             fi
 
-  store-pygrackle-suite-gold-standard-answers:
-    description: "Store the pygrackle test answers"
+  store-gracklepy-suite-gold-standard-answers:
+    description: "Store the gracklepy test answers"
     parameters:
       gold-standard-tag:
         description: "The gold-standard to use for generating the answers"
@@ -206,17 +206,17 @@ commands:
           name: "Build Pygrackle from Gold-Standard Commit (<< parameters.gold-standard-tag >>)"
           command: |
             source $HOME/venv/bin/activate
-            pip uninstall --yes pygrackle # it's ok if pygrackle wasn't installed yet
+            pip uninstall --yes gracklepy # it's ok if gracklepy wasn't installed yet
             git checkout << parameters.gold-standard-tag >>
             pip install -e .
-      - run-pygrackle-tests:
+      - run-gracklepy-tests:
           omp: 'false'
-          build_kind: 'standalone-pygrackle'
+          build_kind: 'standalone-gracklepy'
           generate: 'true'
       - run:
           command: |
             source $HOME/venv/bin/activate
-            pip uninstall --yes pygrackle
+            pip uninstall --yes gracklepy
 
 
   build-docs:
@@ -261,35 +261,35 @@ jobs:
       - install-dependencies
       - lint
       - download-test-data
-      - store-pygrackle-suite-gold-standard-answers
+      - store-gracklepy-suite-gold-standard-answers
 
       - run:
           name: "Build Standalone Pygrackle from the commit that triggered CI."
           command: |
             source $HOME/venv/bin/activate
             git checkout $CIRCLE_BRANCH
             pip install -e .
-      - run-pygrackle-tests:
+      - run-gracklepy-tests:
           omp: 'false'
-          build_kind: 'standalone-pygrackle'
+          build_kind: 'standalone-gracklepy'
           generate: 'false'
 
-      # run pygrackle-test (without answer-tests) on latest commit (CMake-build)
+      # run gracklepy-test (without answer-tests) on latest commit (CMake-build)
       - install-grackle:
           omp: 'false'
           classic_build: 'false'
           tag: $CIRCLE_BRANCH
       - run:
-          name: "pygrackle-tests (no answer-tests) on latest commit (corelib manually built with CMake)"
+          name: "gracklepy-tests (no answer-tests) on latest commit (corelib manually built with CMake)"
           command: source $BASH_ENV && source $HOME/venv/bin/activate && py.test
 
-      # run full pygrackle test-suite on latest commit (classic-build)
+      # run full gracklepy test-suite on latest commit (classic-build)
       - install-grackle:
           omp: 'false'
           classic_build: 'true'
           tag: $CIRCLE_BRANCH
       - run:
-          name: "pygrackle-tests (no answer-tests) on latest commit (corelib manually created with classic-build)"
+          name: "gracklepy-tests (no answer-tests) on latest commit (corelib manually created with classic-build)"
           command: source $BASH_ENV && source $HOME/venv/bin/activate && py.test
 
   corelib-tests:

README.rst

@@ -13,7 +13,7 @@ Grackle
 
 `Documentation <https://grackle.readthedocs.io/en/latest/>`__ |
 `Installation <https://grackle.readthedocs.io/en/latest/Installation.html>`__ |
-`Pygrackle Installation <https://grackle.readthedocs.io/en/latest/Python.html>`__ |
+`Gracklepy Installation <https://grackle.readthedocs.io/en/latest/Python.html>`__ |
 `Usage Guide <https://grackle.readthedocs.io/en/latest/Interaction.html>`__ |
 `Integration Guide <https://grackle.readthedocs.io/en/latest/Integration.html>`__ |
 `Contributing <https://grackle.readthedocs.io/en/latest/Contributing.html>`__ |
@@ -23,7 +23,7 @@ Grackle
 
 Grackle is a chemistry and radiative cooling library for astrophysical simulations and models.
 The core library provides interfaces for C, C++ and Fortran simulation codes.
-The project also offers the Pygrackle package to provide Python bindings.
+The project also offers the Gracklepy package to provide Python bindings.
 
 Features
 --------
@@ -86,7 +86,7 @@ To install Grackle, invoke ``cmake --install ./build [--prefix <prefix/path>]``
 For more details **(especially if you encounter any errors),** see our comprehensive `Installation Guide <https://grackle.readthedocs.io/en/latest/Installation.html>`__.
 It provides more context for inexperienced CMake users, describes additional configuration options (relevant if you encounter issues), and describes Grackle's "classic" build-system.
 
-Building Pygrackle from Source
+Building Gracklepy from Source
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Once you have a Fortran compiler and a copy of HDF5 (1.6 or newer), simply invoke the following from the root of the Grackle repository
@@ -95,7 +95,10 @@ Once you have a Fortran compiler and a copy of HDF5 (1.6 or newer), simply invok
 
    ~/grackle $ pip install .
 
-For more about installation see our `Pygrackle installation guide <https://grackle.readthedocs.io/en/latest/Python.html>`__.
+For more about installation see our `Gracklepy installation guide <https://grackle.readthedocs.io/en/latest/Python.html>`__.
+
+**NOTE:** Gracklepy was formerly known as Pygrackle.
+If you previously installed Pygrackle, you should uninstall it before you install GracklePy.
 
 Getting Started
 ---------------
@@ -105,7 +108,7 @@ To help you start using Grackle, we provide:
 - a `Usage Guide <https://grackle.readthedocs.io/en/latest/Interaction.html>`__
 - example Grackle programs written in `C, C++, and Fortran <https://github.com/grackle-project/grackle/tree/main/src/example>`__
 - an `Integration Guide <https://grackle.readthedocs.io/en/latest/Integration.html>`__ (for linking Grackle)
-- a curated `guide <https://grackle.readthedocs.io/en/latest/Python.html#running-the-example-scripts>`__ for the Pygrackle examples
+- a curated `guide <https://grackle.readthedocs.io/en/latest/Python.html#running-the-example-scripts>`__ for the Gracklepy examples
 
 Contributing
 ------------

doc/source/Contributing.rst

@@ -12,7 +12,7 @@ This section provides a short list of tasks to complete when a new field is intr
    (i) the field is initialized to the appropriate default value.
    (ii) the new field and its value are printed when ``grackle_verbose = 1``
    (iii) the field can be accessed by the functions providing the dynamic access to members of :c:data:`chemistry_data` (see :ref:`dynamic-api`)
-   (iv) the new field is accessible from Pygrackle (because that interface uses the functions providing dynamic access)
+   (iv) the new field is accessible from Gracklepy (because that interface uses the functions providing dynamic access)
 
 2. Update the fortran definition for the ``grackle_chemistry_data`` type (in ``src/clib/grackle_fortran_interface.def``). This type must exactly match the definition of :c:data:`chemistry_data` and is used to integrate Grackle into simulation codes written in Fortran.
 

doc/source/Installation.rst

@@ -720,7 +720,7 @@ Compiler Toolchain Compatability
 
 As a general rule of thumb, the easiest, most reliable thing to do is  to ensure that Grackle is built with the same compiler toolchain (or a compatible one) as the
 
-* the downstream application itself (whether it's a simulation code or pygrackle)
+* the downstream application itself (whether it's a simulation code or gracklepy)
 * any other dependencies of the application (whether it's other software libraries or other python extension-modules loaded at the same time).
 
 This is only something you need to consider on platforms with multiple compiler toolchains present.