Automatic developer environment creation

.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# Migration commits for linting, formatting
+a008125e8203ae7245af8af945846ae54e0d51c4
+7d9f5008ae77a7ded8c721e952f958e56c4174f5
+977964573e4260c096d6f74ec908da7d810f1e80

.github/codecov.yml

@@ -16,4 +16,4 @@ coverage:
         # extension:
         # https://github.com/codecov/browser-extension
         target: auto
-        threshold: 1%
+        threshold: 1%

.github/dependabot.yml

@@ -5,4 +5,4 @@ updates:
   schedule:
     interval: daily
     time: "09:00"
-  open-pull-requests-limit: 10
+  open-pull-requests-limit: 10

.github/workflows/dev_tests.yaml

@@ -0,0 +1,48 @@
+name: Run development tests
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+  schedule:
+    # Run every Sunday at 03:53 UTC
+    - cron: 53 3 * * 0
+
+jobs:
+  dev_tests:
+    runs-on: "${{ matrix.os }}"
+    strategy:
+      matrix:
+        python-version: [
+          "3.11",
+          "3.12",
+          "3.13",
+        ]
+
+        os:
+          - ubuntu-latest
+          - macos-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          channels: conda-forge
+          conda-remove-defaults: true
+          miniforge-version: latest
+
+      - name: Install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: |
+            3.11
+            3.12
+            3.13
+
+
+      - name: Run dev tests
+        run: |
+          python -m pip install nox
+          nox -s run_dev_tests -- -vv

.github/workflows/lint.yml

@@ -0,0 +1,43 @@
+# Linting and format-checking workflow for the repository.
+#
+# Behavior in this file, other than setup, is controlled in the file
+# .pre-commit-config.yaml in the top directory of the repository.
+#
+# Any automations should be added to that file. This check runs over the entire
+# repository, not just changes.
+name: Lint repository
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+  schedule:
+    # Run every Sunday at 03:53 UTC
+    - cron: 53 3 * * 0
+
+jobs:
+  lint:
+    runs-on: "${{ matrix.os }}"
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+        os:
+          - ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+
+      - name: Install packages
+        shell: bash -l {0}
+        run: python -m pip install nox
+
+      - name: Run pre-commit via nox
+        shell: bash -l {0}
+        run: |
+          nox -s lint

.github/workflows/unit-tests.yml

@@ -9,7 +9,7 @@ on:
     - cron: 53 3 * * 0
 
 jobs:
-  tests:
+  unit_tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:

.jenkins/Jenkinsfile_conda

@@ -148,4 +148,3 @@ pipeline {
         }
     }
 }
-

.jenkins/scripts/setup_dirs.sh

@@ -17,4 +17,3 @@ if [[ -n "${DRAGONS_TEST_OUT-}" ]]; then
 else
     echo "DRAGONS_TEST_OUT is not set, so not deleting it"
 fi
-

.jenkins/scripts/update_files_permissions.sh

@@ -8,4 +8,3 @@ chmod -Rv 775 $DRAGONS_TEST_INPUTS || echo 1
 chmod -Rv 775 $DRAGONS_TEST_OUTPUTS || echo 1
 
 chmod -Rv 775 $DRAGONS_TEST_REFS || echo 1
-

.pre-commit-config.yaml

@@ -0,0 +1,68 @@
+# pre-commit configuration for DRAGONS
+#
+# Please follow these guidelines:
+#
+# 1) All linting behavior can & should be defined in this file. For example,
+#    that includes:
+#
+#    + Formatting
+#    + Syntax/type checks
+#    + Commit protections/standards
+#
+# 2) Do not include any tests involving the execution of this software, under
+#    any circumstances.
+#
+# 3) This should be a superset of the NOIRLab Python Standard, which can be
+#    found here:
+#
+#    https://github.com/teald/python-standard-template/blob/main/.pre-commit-config.yaml
+default_stages: [pre-commit]
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-yaml
+  - id: check-json
+  - id: check-toml
+  - id: check-docstring-first
+    exclude: "archived/"
+  - id: check-case-conflict
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-symlinks
+  - id: check-vcs-permalinks
+  - id: forbid-submodules
+
+- repo: https://github.com/executablebooks/mdformat
+  rev: 0.7.18  # Use the ref you want to point at
+  hooks:
+  - id: mdformat
+    # Optionally add plugins
+    additional_dependencies:
+    - mdformat-gfm
+    - mdformat-black
+    args: ['--wrap=80']
+
+# Below is the formatter (to be turned on after pyproject.toml update)
+# # Mirror uses compiled black, so faster.
+# - repo: https://github.com/psf/black-pre-commit-mirror
+#   rev: 24.8.0
+#   hooks:
+#     - id: black
+#       # It is recommended to specify the latest version of Python
+#       # supported by your project here, or alternatively use
+#       # pre-commit's default_language_version, see
+#       # https://pre-commit.com/#top_level-default_language_version
+#       language_version: python3.12
+#       exclude: "archived/"
+
+
+# Below is linter (to be turned on after pyproject.toml update)
+# - repo: https://github.com/astral-sh/ruff-pre-commit
+#   # Ruff version.
+#   rev: v0.8.3
+#   hooks:
+#     # Run the linter.
+#     - id: ruff
+#       exclude: "archived/"

.readthedocs.yaml

@@ -27,4 +27,4 @@ sphinx:
 python:
    install:
    - requirements: requirements.txt
-   - requirements: doc/requirements.txt
+   - requirements: doc/requirements.txt

LICENSE

@@ -31,4 +31,3 @@ GOODS OR 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

@@ -1,5 +1,3 @@
-
-
 <table border="0">
 <tr>
   <td rowspan="2"><img src="./graphics/DRAGONS-Iconblue.png" width="100" height="100"></td>
@@ -11,18 +9,19 @@
 </table>
 
 # Current Status
-**The stable version is v3.2.2.**  
 
+**The stable version is v3.2.2.**
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13821517.svg)](https://doi.org/10.5281/zenodo.13821517) DRAGONS is distributed as a conda package, *dragons*, and it is 
-included in the conda *gemini* stack.
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13821517.svg)](https://doi.org/10.5281/zenodo.13821517)
+DRAGONS is distributed as a conda package, *dragons*, and it is included in the
+conda *gemini* stack.
 
 Version 3.2 is recommend for the reduction of **imaging** data from Gemini's
 current facility instruments: GMOS, NIRI, Flamingos-2, and GSAOI, for the
 reduction of GMOS longslit spectroscopy data, and the reduction of GHOST data.
 
-To reduce other types of Gemini spectroscopy data, please continue to use 
-the [Gemini IRAF package](https://www.gemini.edu/observing/phase-iii/reducing-data/gemini-iraf-data-reduction-software).
+To reduce other types of Gemini spectroscopy data, please continue to use the
+[Gemini IRAF package](https://www.gemini.edu/observing/phase-iii/reducing-data/gemini-iraf-data-reduction-software).
 
 To install DRAGONS:
 
@@ -37,49 +36,49 @@ $ conda config --add channels conda-forge
 $ conda config --add channels http://astroconda.gemini.edu/public
 ```
 
+A list of changes since 3.1 can be found in the
+[Change Logs](https://dragons.readthedocs.io/en/v3.2.0/changes.html).
 
-A list of changes since 3.1 can be found in the [Change Logs](https://dragons.readthedocs.io/en/v3.2.0/changes.html).
+______________________________________________________________________
 
----
 # What is DRAGONS
-DRAGONS is a platform for the reduction and processing of astronomical data.
-The DRAGONS meta-package includes an infrastructure for automation of the
-processes and algorithms for processing of astronomical data, with focus on the 
-reduction of Gemini data.
 
+DRAGONS is a platform for the reduction and processing of astronomical data. The
+DRAGONS meta-package includes an infrastructure for automation of the processes
+and algorithms for processing of astronomical data, with focus on the reduction
+of Gemini data.
 
----
+______________________________________________________________________
 
 # Documentation
+
 Documentation on DRAGONS v3.2 is available on "readthedocs" at:
 
-* https://dragons.readthedocs.io/en/v3.2.2/
+- https://dragons.readthedocs.io/en/v3.2.2/
 
 There your will find manuals for Astrodata and the Recipe System, and hands-on
 tutorials on reducing Gemini imaging data with DRAGONS.
 
-Gemini users with imaging data to reduce should pick the tutorial discussing
-the reduction of data from the appropriate instrument.  
+Gemini users with imaging data to reduce should pick the tutorial discussing the
+reduction of data from the appropriate instrument.
 
-Software developers should start with the Astrodata and Recipe System
-manuals.
+Software developers should start with the Astrodata and Recipe System manuals.
 
----
+______________________________________________________________________
 
 # Setting up a development environment
 
-To run checkouts, first set up a development conda environment.  This is what
-we are using at this time for the `master` branch and the `release/3.2.x` 
-branches.
+To run checkouts, first set up a development conda environment. This is what we
+are using at this time for the `master` branch and the `release/3.2.x` branches.
 
 ```
 $ conda create -n dgdev3.10_20240401 python=3.10 astropy=6 astroquery matplotlib numpy psutil pytest python-dateutil requests scikit-image scipy sextractor sqlalchemy ds9 gwcs specutils sphinx sphinx_rtd_theme bokeh holoviews cython future astroscrappy=1.1 fitsverify imexam
 $ conda activate dgdev3.10_20240401
 $ pip install git+https://github.com/GeminiDRSoftware/GeminiObsDB.git@release/1.0.x
 $ pip install git+https://github.com/GeminiDRSoftware/GeminiCalMgr.git@release/1.1.x
 ```
-Dependencies change all the time and can break the development environment
-or cause problems when conda tries to find a solution for the dependencies. 
-This not guaranteed to work flawlessly, you might have to adjust version
-requirements.
 
+Dependencies change all the time and can break the development environment or
+cause problems when conda tries to find a solution for the dependencies. This
+not guaranteed to work flawlessly, you might have to adjust version
+requirements.