Initial commit with changes to template

SPiN-Lab · Jul 19, 2022 · cb1a092 · cb1a092
1 parent 83e1210
commit cb1a092
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Showing 22 changed files with 182 additions and 208 deletions.
diff --git a/.circleci/artifact_path b/.circleci/artifact_path
@@ -1 +1 @@
-0/tmp/src/template-package/docs/_build/html/index.html
+0/tmp/src/tedana_regressors/docs/_build/html/index.html
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,20 +6,19 @@ version: 2.1
 orbs:
   codecov: codecov/[email protected]
 jobs:
-
   py36_unittest:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
       - checkout
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/template-package
-      - run:  # will overwrite template-package installation each time
+            - src/tedana_regressors
+      - run: # will overwrite tedana_regressors installation each time
           name: Generate environment
-          command:  |
+          command: |
             if [[ -e /opt/conda/envs/py36_env ]]; then
                 echo "Restoring environment from cache"
                 source activate py36_env
@@ -31,25 +30,25 @@ jobs:
             python setup.py install --user
       - run:
           name: Run tests
-          command:  |
+          command: |
             apt-get update
             apt-get install -yqq make
             source activate py36_env
             make unittest
 
   py37_unittest:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
       - checkout
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/template-package
-      - run:  # will overwrite template-package installation each time
+            - src/tedana_regressors
+      - run: # will overwrite tedana_regressors installation each time
           name: Generate environment
-          command:  |
+          command: |
             if [[ -e /opt/conda/envs/py37_env ]]; then
                 echo "Restoring environment from cache"
                 source activate py37_env
@@ -61,25 +60,25 @@ jobs:
             python setup.py install --user
       - run:
           name: Run tests
-          command:  |
+          command: |
             apt-get update
             apt-get install -yqq make
             source activate py37_env
             make unittest
 
   py38_unittest:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
       - checkout
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/template-package
-      - run:  # will overwrite template-package installation each time
+            - src/tedana_regressors
+      - run: # will overwrite tedana_regressors installation each time
           name: Generate environment
-          command:  |
+          command: |
             if [[ -e /opt/conda/envs/py38_env ]]; then
                 echo "Restoring environment from cache"
                 source activate py38_env
@@ -92,27 +91,27 @@ jobs:
             python setup.py install --user
       - run:
           name: Run tests
-          command:  |
+          command: |
             apt-get update
             apt-get install -yqq make
             source activate py38_env
             make unittest
 
   py39_env:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
       - checkout
       - persist_to_workspace:
           root: /tmp
           paths:
-              - src/template-package
-      - restore_cache:  # ensure this step occurs *before* installing dependencies
-          key: deps1-{{ checksum "template-package/setup.cfg" }}-{{ checksum "setup.py" }}
-      - run:  # will overwrite template-package installation each time
+            - src/tedana_regressors
+      - restore_cache: # ensure this step occurs *before* installing dependencies
+          key: deps1-{{ checksum "tedana_regressors/setup.cfg" }}-{{ checksum "setup.py" }}
+      - run: # will overwrite tedana_regressors installation each time
           name: Generate environment
-          command:  |
+          command: |
             if [[ -e /opt/conda/envs/py39_env ]]; then
                 echo "Restoring environment from cache"
                 source activate py39_env
@@ -122,40 +121,40 @@ jobs:
                 pip install -e .[tests,doc]
             fi
             python setup.py install --user
-      - save_cache:  # environment cache tied to requirements
-          key: deps1-{{ checksum "template-package/setup.cfg" }}-{{ checksum "setup.py" }}
+      - save_cache: # environment cache tied to requirements
+          key: deps1-{{ checksum "tedana_regressors/setup.cfg" }}-{{ checksum "setup.py" }}
           paths:
             - "/opt/conda/envs/py39_env"
 
   py39_unittest_and_coverage:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
-      - attach_workspace:  # get template-package
+      - attach_workspace: # get tedana_regressors
           at: /tmp
-      - restore_cache:  # load environment
-          key: deps1-{{ checksum "template-package/setup.cfg" }}-{{ checksum "setup.py" }}
+      - restore_cache: # load environment
+          key: deps1-{{ checksum "tedana_regressors/setup.cfg" }}-{{ checksum "setup.py" }}
       - run:
           name: Run tests and compile coverage
-          command:  |
+          command: |
             apt-get update
             apt-get install -yqq make
             apt-get install -yqq curl
             source activate py39_env
             make unittest
       - codecov/upload:
-          file: /tmp/src/template-package/coverage.xml
+          file: /tmp/src/tedana_regressors/coverage.xml
 
   build_docs:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
-      - attach_workspace:  # get template-package
+      - attach_workspace: # get tedana_regressors
           at: /tmp
-      - restore_cache:  # load environment
-          key: deps1-{{ checksum "template-package/setup.cfg" }}-{{ checksum "setup.py" }}
+      - restore_cache: # load environment
+          key: deps1-{{ checksum "tedana_regressors/setup.cfg" }}-{{ checksum "setup.py" }}
       - run:
           name: Build documentation
           command: |
@@ -165,22 +164,22 @@ jobs:
             make -C docs html
           no_output_timeout: 30m
       - store_artifacts:
-          path: /tmp/src/template-package/docs/_build/html
+          path: /tmp/src/tedana_regressors/docs/_build/html
 
   style_check:
-    working_directory: /tmp/src/template-package
+    working_directory: /tmp/src/tedana_regressors
     docker:
       - image: continuumio/miniconda3
     steps:
-      - attach_workspace:  # get template-package
+      - attach_workspace: # get tedana_regressors
           at: /tmp
-      - restore_cache:  # load environment
-          key: deps1-{{ checksum "template-package/setup.cfg" }}-{{ checksum "setup.py" }}
+      - restore_cache: # load environment
+          key: deps1-{{ checksum "tedana_regressors/setup.cfg" }}-{{ checksum "setup.py" }}
       - run:
           name: Linting
-          command:  |
+          command: |
             source activate py39_env
-            flake8 /tmp/src/template-package/template-package
+            flake8 /tmp/src/tedana_regressors/tedana_regressors
       - store_artifacts:
           path: /tmp/data/lint
 

diff --git a/.codecov.yml b/.codecov.yml
@@ -15,7 +15,6 @@ coverage:
         threshold: 0
 
 ignore:
-  - 'template-package/tests/'
-  - 'template-package/due.py'
-  - 'template-package/_version.py'
-  - 'template-package/info.py'
+  - "tedana_regressors/tests/"
+  - "tedana_regressors/_version.py"
+  - "tedana_regressors/info.py"
diff --git a/.gitattributes b/.gitattributes
@@ -1 +1 @@
-template-package/_version.py export-subst
+tedana_regressors/_version.py export-subst
diff --git a/.github/config.yml b/.github/config.yml
@@ -4,11 +4,11 @@
 newPRWelcomeComment: >
   Thanks for opening this pull request!
   We have detected this is the first time you have contributed
-  to *template-package*.
+  to *tedana_regressors*.
 
-  We invite you to list yourself as a *template-package* contributor, so if your name
+  We invite you to list yourself as a *tedana_regressors* contributor, so if your name
   is not already mentioned, please modify the
-  [``.zenodo.json``](https://github.com/ME-ICA/template-package/blob/main/.zenodo.json).
+  [``.zenodo.json``](https://github.com/ME-ICA/tedana_regressors/blob/main/.zenodo.json).
 
   Of course, if you want to opt out this time there is no
   problem at all with adding your name later.

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,5 +1,5 @@
 <!---
-This is a suggested pull request template for template-package.
+This is a suggested pull request template for tedana_regressors.
 It's designed to capture information we've found to be useful in reviewing pull requests.
 
 If there is other information that would be helpful to include, please don't hesitate to add it!

diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,2 +1,2 @@
 include versioneer.py
-include template-package/_version.py
+include tedana_regressors/_version.py
diff --git a/Makefile b/Makefile
@@ -5,14 +5,14 @@ all_tests: lint unittest integrationtest
 help:
 	@echo "Please use 'make <target>' where <target> is one of:"
 	@echo "  lint			to run flake8 on all Python files"
-	@echo "  unittest		to run unit tests on template-package"
+	@echo "  unittest		to run unit tests on tedana_regressors"
 	@echo "  integrationtest		to run integration tests"
 
 lint:
-	@flake8 template-package
+	@flake8 tedana_regressors
 
 unittest:
-	@py.test -m "not integration" --cov-append --cov-report xml --cov-report term-missing --cov=template-package template-package
+	@py.test -m "not integration" --cov-append --cov-report xml --cov-report term-missing --cov=tedana_regressors tedana_regressors
 
 performancetest:
-	@py.test -m "integration" --cov-append --cov-report xml --cov-report term-missing --cov=template-package template-package
+	@py.test -m "integration" --cov-append --cov-report xml --cov-report term-missing --cov=tedana_regressors tedana_regressors
diff --git a/README.md b/README.md
@@ -1,17 +1,18 @@
-# template-package
+# tedana_regressors
+
 A template repo to use for new repositories.
 
-[![Latest Version](https://img.shields.io/pypi/v/template-package.svg)](https://pypi.python.org/pypi/template-package/)
-[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/template-package.svg)](https://pypi.python.org/pypi/template-package/)
+[![Latest Version](https://img.shields.io/pypi/v/tedana_regressors.svg)](https://pypi.python.org/pypi/tedana_regressors/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/tedana_regressors.svg)](https://pypi.python.org/pypi/tedana_regressors/)
 [![DOI](https://zenodo.org/badge/111111.svg)](https://zenodo.org/badge/latestdoi/111111)
 [![License](https://img.shields.io/badge/License-LGPL%202.1-blue.svg)](https://opensource.org/licenses/LGPL-2.1)
-[![CircleCI](https://circleci.com/gh/ME-ICA/template-package.svg?style=shield)](https://circleci.com/gh/ME-ICA/template-package)
-[![Documentation Status](https://readthedocs.org/projects/template-package/badge/?version=latest)](http://template-package.readthedocs.io/en/latest/?badge=latest)
-[![Codecov](https://codecov.io/gh/me-ica/template-package/branch/main/graph/badge.svg)](https://codecov.io/gh/me-ica/template-package)
+[![CircleCI](https://circleci.com/gh/ME-ICA/tedana_regressors.svg?style=shield)](https://circleci.com/gh/ME-ICA/tedana_regressors)
+[![Documentation Status](https://readthedocs.org/projects/tedana_regressors/badge/?version=latest)](http://tedana_regressors.readthedocs.io/en/latest/?badge=latest)
+[![Codecov](https://codecov.io/gh/me-ica/tedana_regressors/branch/main/graph/badge.svg)](https://codecov.io/gh/me-ica/tedana_regressors)
 
 ## Instructions
 
-1. Replace `template-package` with the new repo name across the whole repository.
+1. Replace `tedana_regressors` with the new repo name across the whole repository.
 1. Enable the GitHub repository on Zenodo.
 1. Set up the GitHub repository on CircleCI.
 1. Set up the GitHub repository on ReadTheDocs.

diff --git a/docs/Makefile b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = template-package
+SPHINXPROJ    = tedana_regressors
 SOURCEDIR     = .
 BUILDDIR      = _build
 

diff --git a/docs/api.rst b/docs/api.rst
@@ -1,6 +1,6 @@
 .. _api_ref:
 
-.. currentmodule:: template-package
+.. currentmodule:: tedana_regressors
 
 ###
 API
@@ -10,21 +10,21 @@ API
 .. _api_module_ref:
 
 **************************************************
-:mod:`template-package.module`: Module description
+:mod:`tedana_regressors.module`: Module description
 **************************************************
 
-.. automodule:: template-package.module
+.. automodule:: tedana_regressors.module
    :no-members:
    :no-inherited-members:
 
-.. currentmodule:: template-package.module
+.. currentmodule:: tedana_regressors.module
 
 .. autosummary::
    :toctree: generated/
    :template: class.rst
 
-   template-package.module.Class
+   tedana_regressors.module.Class
 
    :template: function.rst
 
-   template-package.module.function
+   tedana_regressors.module.function