Merge pull request #590 from sbillinge/jan25

added pokratath etc..  Also prettify citations

Author: sbillinge

.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 +1,55 @@
+;; 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
+
+;; The facility not the attitude
+SLAC
+
+;; The chemicals
+Nd
+ThSe
+Te
+NWO
+AFE
+
+;; The names of collaborators
+Nam
+Skelton
+Tennant
+BASF
+Joo
+Hart
+Comin
+Stach
+Comor
+Flor
+Winn
+Studi
+
+;; Whet as in appetite
+whet
+
+;; journal abbreviations
+Commun
+Ser
+bridg
+slac
+SHS
+stach
+selt
+als
+basf
+
+;; citation things
+annote
+
+;; the state
+ND

.flake8

@@ -0,0 +1,13 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    doc/source/conf.py
+max-line-length = 115
+# 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

.github/workflows/publish.yml

@@ -1,19 +1,18 @@
-name: Publish Group Webiste
+name: Publish Group Website
 
 on:
   push:
     branches:
       - main
   workflow_dispatch:
 
-
 jobs:
   publish:
     name: Miniconda ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
-        matrix:
-            os: ["ubuntu-latest"]
+      matrix:
+        os: ['ubuntu-latest']
     steps:
       - name: check out rg-db-public
         uses: actions/checkout@v3

.pre-commit-config.yaml

@@ -0,0 +1,70 @@
+default_language_version:
+  python: python3
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+        exclude: '^{{ cookiecutter.github_repo_name }}/.*\.yml$' # {{ cookiecutter.github_repo_name }} contains jinja variables in .yml, hook fails
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+        exclude: '^{{ cookiecutter.github_repo_name }}/.*\.toml$' # {{ cookiecutter.github_repo_name }} contains jinja variables in pyproject.toml, hook fails
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+        exclude: '^({{ cookiecutter.github_repo_name }}/.*\.py|hooks/post_gen_project\.py)$' # {{ cookiecutter.github_repo_name }} contains jinja variables in .py, hook fails. hooks/post_gen_project.py contains jinja variables of # (c) {% now 'utc', '%Y' %} which is not a valid black format
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        exclude: '^({{ cookiecutter.github_repo_name }}/.*\.py|hooks/post_gen_project\.py)$' # Same comment as black above
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        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
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

.prettierignore

@@ -0,0 +1,2 @@
+# Ignore jinja2 variables within the project
+{{ cookiecutter.github_repo_name }}

.prettierrc

@@ -0,0 +1,12 @@
+{
+  "overrides": [
+    {
+      "files": "*.yml",
+      "options": {
+        "singleQuote": true,
+        "proseWrap": "preserve"
+      }
+    }
+  ],
+  "printWidth": 115
+}

LICENSE

@@ -21,4 +21,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-

README.md

@@ -1,24 +1,26 @@
 ![CI](https://github.com/billingegroup/rg-db-public/actions/workflows/main.yml/badge.svg)
+
 # rg-db-public
-Billinge Group Public Research Group Database
 
+Billinge Group Public Research Group Database
 
 This repo contains public facing data from the Billinge Group in the Applied
-Physics and Applied Mathematics department at Columbia University.  It will be used 
+Physics and Applied Mathematics department at Columbia University. It will be used
 to build the group dynamic web-site at `https://billingegroup.github.io` using
-regolith (https://github.com/regro/regolith).  Regolith will also build 
+regolith (https://github.com/regro/regolith). Regolith will also build
 people's public facing cv's and publication lists from this information here.
 
 You need to be a current or former member of the Billinge Group at Columbia
-University to update entries in this database.  Please reach out to Prof. 
+University to update entries in this database. Please reach out to Prof.
 Billinge (sb2896@columbia.edu) if you are interested in joining the group.
 
-For group members, the current branching workflow is to directly clone this 
+For group members, the current branching workflow is to directly clone this
 repo to your local, make pushes to branches directly on this GitHub repository
-and create a PR into the default branch `main`.  We are no longer using a
+and create a PR into the default branch `main`. We are no longer using a
 forking workflow (i.e., don't create a fork).
 
 These commands might help you get going:
+
 ```
 cd dbs
 git clone git@github.com:Billingegroup/rg-db-public.git
@@ -27,28 +29,31 @@ git add <files>
 git commit -m "an informative commit message"
 git push -u origin <branch_name>
 ```
-then go to GitHub to open a PR into `main`, so it will look like 
+
+then go to GitHub to open a PR into `main`, so it will look like
 `base:main <- compare:<branch_name>`
 
 Do not ever merge directly into main (actually you shouldn't be able to on GitHub).
-This merge will be done by Prof. Billinge after review.   
+This merge will be done by Prof. Billinge after review.
 
 To prevent nasty accidents,
-1. create a file in `rg-db-public/.git/hooks` called `pre-commit` and copy-paste the 
- following into it and save it
+
+1. create a file in `rg-db-public/.git/hooks` called `pre-commit` and copy-paste the
+   following into it and save it
 2. Mark the new file as executable: `chmod +x rg-db-public/.git/hooks/pre-commit`.
 
-This will prevent you accidentally making local changes to your main branch that won't 
+This will prevent you accidentally making local changes to your main branch that won't
 be mergeable.
+
 ```
 #!/bin/sh
 #
 # To prevent accidental commits to main,
-# copy this file, with name 
-#    "pre-commit" 
-# to the 
+# copy this file, with name
+#    "pre-commit"
+# to the
 #    .git/hooks (notice the dot in front of git)
-# directory in this 
+# directory in this
 # repo
 
 branch="$(git rev-parse --abbrev-ref HEAD)"