Cookie into main (#1212)

* Remove files no longer used (#1176)

* cookierelease: copied over index.rst (#1175)

* copied over index.rst

* as and cj to authors in docs.

---------

Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com>

* edit pyproject.toml per PR#1183 (#1187)

* trim trailing whitespaces (#1190)

* Codespell - edit typos (#1189)

* correct spelling in CHANGELOG.rst

* edit typos

* add tool.codespell section to pyproject.toml

* add ignore_lines and ignore_words

* add ignore_words

* add codespell to pre-commit

* add more file extensions to skip

* fix typo

* add more words to ignore

* Recut - add github CI files, remove github deploy key, flake8 latest (#1191)

* Add github CI, remove github deploy key, flake8 latest

* Add requires-python = ">=3.11, <3.14" in pyproject.toml

* Remove 3.10 classifier in pyproject.toml

* remove duplicate codespell lines (#1193)

* run tests on cookie, not on main in pr (#1194)

* Cookie: restore old txt files (so pytest is passing) (#1198)

* remove duplicate codespell lines

* exclude txt in trailing-whitespace fixes

* restore old version of txt files with whitespaces

* Configure non-reusable Python 3.11 Test on PR GitHub CI (#1203)

* Add Python 3.11 test on PR and install libgtk to build wxpython

* Use regolith instead of labpdfproc name

* change position values in grants to remove warnings in tests (#1205)

* change position values in grants to remove warnings in tests

* for 3.11 we don't bave to build wx from sources

* try again to get gooey going without wx build

* Cookie move tests (#1199)

* flake8 exclude test_helpers.py

* merge two versions of conftest.py

* make flake8 exclude test_helpers.py

* make flake8 ignore test_helpers.py

* move test_helpers

* move the remaining tests files

* deletions from src/regolith/tests

* make flake8 exclude test_commands.py

* make flake8 ignore test_commands

* ignore test_helpers and test_commands

* ignore test_helpers and test_commands

* comment out import conftest

* fix typos

* fix minor typo

* codespell ignore Ond

* fix minor typo

* Re-cun CI with empty commit

* fix matplotlib plot_date warnings (#1207)

---------

Co-authored-by: Sangjoon Bob Lee <bob@boblee.io>
Co-authored-by: tinatn29 <77407300+tinatn29@users.noreply.github.com>

.codecov.yml

@@ -1,34 +1,14 @@
-# codecov can find this file anywhere in the repo, so we don't need to clutter
-# the root folder.
-#comment: false
-
-codecov:
-  notify:
-    require_ci_to_pass: no
-
 coverage:
   status:
-    patch:
+    project:  # more options at https://docs.codecov.com/docs/commit-status
       default:
-        target: '70'
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: failure
-    project:
-      default: false
-      library:
-        target: auto
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: error
-        paths: '!*/tests/.*'
-
-      tests:
-        target: 97.9%
-        paths: '*/tests/.*'
-        if_not_found: success
-
-flags:
-  tests:
-    paths:
-      - tests/
+        target: auto # use the coverage from the base commit, fail if coverage is lower
+        threshold: 0%  # allow the coverage to drop by
+
+comment:
+  layout: " diff, flags, files"
+  behavior: default
+  require_changes: false
+  require_base: false  # [true :: must have a base report to post]
+  require_head: false  # [true :: must have a head report to post]
+  hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,27 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro
+
+;; variable names
+stati
+convertor
+dploy
+pres
+Ond
+
+;; package name
+rever
+
+;; people.rst manually allows 'programer' as a variation of 'programmer'
+programer
+
+;; suffix for dates
+nd

.flake8

@@ -6,8 +6,6 @@ exclude =
     dist,
     doc/source/conf.py
 max-line-length = 115
-# Ignore some style 'errors' produced while formatting by 'black' (see link below)
+# Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
 extend-ignore = E203
-per-file-ignores =
-    src/regolith/tests/test_helpers.py: E501

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -13,10 +13,16 @@ assignees: ""
 - [ ] License information is verified as correct. If you are unsure, please comment below.
 - [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
   missing), tutorials, and other human written text is up-to-date with any changes in the code.
-- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated and
-  tested
-- [ ] Successfully run any tutorial examples or do functional testing in some other way.
+- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version
 - [ ] Grammar and writing quality have been checked (no typos).
 
 Please mention @sbillinge when you are ready for release. Include any additional comments necessary, such as
-version information and details about the pre-release.
+version information and details about the pre-release here:
+
+### Post-release checklist
+
+Before closing this issue, please complete the following:
+
+- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README.
+- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.github/workflows/check-news-item.yml

@@ -6,7 +6,7 @@ on:
     - main
 
 jobs:
-  build:
+  check-news-item:
     uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: regolith

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
+  matrix-coverage:
     uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: regolith

.github/workflows/tests-on-pr.yml

@@ -4,13 +4,57 @@ on:
   push:
     branches:
       - main
+      - cookie
   pull_request:
   workflow_dispatch:
 
 jobs:
   validate:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
-    with:
-      project: regolith
-      c_extension: false
-      headless: false
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out regolith repository
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+          python-version: 3.11
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install libgtk for Linux
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgtk-3-dev
+
+      - name: Install regolith and requirements
+        run: |
+          conda install --file requirements/test.txt
+          conda install --file requirements/conda.txt
+          pip install gooey
+          python -m pip install . --no-deps
+
+
+      - name: Validate regolith
+        run: |
+          pytest --cov
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          verbose: true
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -16,6 +16,7 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-toml
@@ -28,6 +29,7 @@ repos:
     rev: 7.0.0
     hooks:
       - id: flake8
+        exclude: ^tests/test_helpers.py$|^tests/test_commands.py$
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
@@ -44,3 +46,9 @@ repos:
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli