JOSS Review Meta-Response

.github/workflows/build.yml

@@ -1,39 +1,40 @@
+---
 name: build
 
-on: [push, pull_request]
-
+on:    # yamllint disable-line rule:truthy
+  push:
+    branches-ignore:
+      - 'false'
+  pull_request:
+    branches-ignore:
+      - 'false'
 jobs:
   build:
-      runs-on: ${{ matrix.os }}
-
-      strategy:
-        matrix:
-          os: [ubuntu-latest]
-
-      env:
-        OS: ${{ matrix.os }}
-        PYTHON: '3.9'
-
-      steps:
-
-        - uses: actions/checkout@v1
-
-        - name: Set up Python
-          uses: actions/setup-python@master
-          with:
-            python-version: 3.9
-
-        - name: Install dependencies
-          run: |
-            python -m pip install --upgrade pip
-            python setup.py install
-        - name: Test and generate coverage report on Linux
-          run: |
-            pip install pytest
-            pip install pytest-cov
-            pytest --cov=./ --cov-report=xml
-        - name: Upload coverage to Codecov
-          uses: codecov/codecov-action@v1
-          with:
-            file: ./coverage.xml
-            fail_ci_if_error: true
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: '3.9'
+
+    steps:
+
+      - uses: actions/checkout@v1
+
+      - name: Set up Python
+        uses: actions/setup-python@master
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python setup.py install
+      - name: Test and generate coverage report on Linux
+        run: |
+          pip install pytest
+          pip install pytest-cov
+          pytest --cov=./ --cov-report=xml

.github/workflows/draft-pdf.yml

@@ -1,5 +1,8 @@
-on: [push]
-
+---
+on:    # yamllint disable-line rule:truthy
+  push:
+    branches-ignore:
+      - '**'
 jobs:
   paper:
     runs-on: ubuntu-latest

.github/workflows/pre-commit.yml

@@ -0,0 +1,23 @@
+---
+name: pre-commit
+
+on:    # yamllint disable-line rule:truthy
+    push:
+        branches-ignore:
+            - 'false'
+    pull_request:
+        branches-ignore:
+            - 'false'
+
+jobs:
+    pre-commit:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v3
+            - uses: actions/setup-python@v4
+              with:
+                  python-version: "3.9"
+            - name: Install pre-commit
+              run: pip install pre-commit
+            - name: Run pre-commit on all files
+              run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -0,0 +1,84 @@
+---
+default_language_version:
+  python: python3
+
+exclude: 'paper/paper.md'
+
+repos:
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.8.0
+    hooks:
+      - id: pyupgrade
+        args: ['--py39-plus']
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: debug-statements
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: rst-inline-touching-normal
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        args: ['--target-version=py39']
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: ['--max-line-length=120', '--extend-ignore=E203,E402,F401,F403']
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ['--profile=black']
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-pyupgrade
+        args: ['--py39-plus']
+        additional_dependencies: ['pyupgrade==3.8.0']
+      - id: nbqa-black
+        additional_dependencies: ['black==23.3.0']
+        args: ['--line-length=88', '--target-version=py39']
+      - id: nbqa-isort
+        additional_dependencies: ['isort==5.12.0']
+        args: ['--profile=black']
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.8
+    hooks:
+      - id: blackdoc
+        additional_dependencies: ['black==23.3.0']
+        args: ['--target-version=py39']
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.32.0
+    hooks:
+      - id: yamllint
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.23.2
+    hooks:
+      - id: check-github-workflows
+  - repo: meta
+    hooks:
+      - id: check-hooks-apply
+      - id: check-useless-excludes
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+    for more information, see https://pre-commit.ci
+  autofix_prs: true
+  autoupdate_branch: ''
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: weekly
+  skip: []
+  submodules: false

CITATION.cff

@@ -23,4 +23,4 @@ authors:
   orcid: "https://orcid.org/0000-0002-7963-6102"
 title: "statemodify: a Python framework to facilitate accessible exploratory modeling for discovering drought vulnerabilities in Colorado’s West Slope river basins"
 doi: 10.5281/zenodo.10258007
-url: "https://github.com/IMMM-SFA/statemodify"
+url: "https://github.com/IMMM-SFA/statemodify"

MANIFEST.in

@@ -1,2 +1,2 @@
 include statemodify/data/*.*
-include statemodify/tests/data/*.*
+include statemodify/tests/data/*.*

README.md

@@ -2,6 +2,7 @@
 [![codecov](https://codecov.io/gh/IMMM-SFA/statemodify/branch/main/graph/badge.svg?token=csQBZMRSdp)](https://codecov.io/gh/IMMM-SFA/statemodify)
 [![Static Badge](https://img.shields.io/badge/Powered%20by-MSDLIVE-blue?label=Powered%20by&color=blue)](https://statemodify.msdlive.org)
 [![DOI](https://zenodo.org/badge/484620418.svg)](https://zenodo.org/doi/10.5281/zenodo.10258007)
+[![pre-commit](https://github.com/IMMM-SFA/statemodify/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/IMMM-SFA/statemodify/actions/workflows/pre-commit.yml)
 
 
 

docs/source/conf.py

@@ -1,21 +1,21 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""Configuration file for the Sphinx documentation builder.
 
-import sys
+For the full list of built-in configuration values, see the documentation:
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
 import os
+import sys
 
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../'))
-sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath("../"))
+sys.path.insert(0, os.path.abspath("../../"))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'statemodify'
-copyright = '2023, Battelle Memorial Institute'
-author = 'Rohini S. Gupta'
+project = "statemodify"
+copyright = "2023, Battelle Memorial Institute"
+author = "Rohini S. Gupta"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -29,29 +29,29 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosectionlabel',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.duration',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
-    'sphinx_autodoc_typehints',
-    'sphinx_click',
-    'sphinx_copybutton',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_autodoc_typehints",
+    "sphinx_click",
+    "sphinx_copybutton",
 ]
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3/', None),
-    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
 }
-intersphinx_disabled_domains = ['std']
+intersphinx_disabled_domains = ["std"]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The main toctree document.
-main_doc = 'index'
+main_doc = "index"
 
 pygments_style = None
 autosummary_generate = True
@@ -60,39 +60,39 @@
 # -- Options for autodoc
 
 # Python methods should be presented in source code order
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 
-html_theme = 'sphinx_book_theme'
+html_theme = "sphinx_book_theme"
 
 html_theme_options = {
-    'logo_only': True,
-    'repository_url': 'https://github.com/IMMM-SFA/statemodify',
-    'use_repository_button': True,
-    'use_issues_button': True,
-    'use_edit_page_button': True,
-    'path_to_docs': 'docs/source',
+    "logo_only": True,
+    "repository_url": "https://github.com/IMMM-SFA/statemodify",
+    "use_repository_button": True,
+    "use_issues_button": True,
+    "use_edit_page_button": True,
+    "path_to_docs": "docs/source",
 }
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = 'statemodify documentation'
+html_title = "statemodify documentation"
 
 # -- Options for EPUB output
-epub_show_urls = 'footnote'
+epub_show_urls = "footnote"
 
 # -- Options for sphinx-copybutton
-copybutton_prompt_text = r'\$ '
+copybutton_prompt_text = r"\$ "
 copybutton_prompt_is_regexp = True
 
 html_show_sourcelink = False
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = 'images/logo_statemodify.png'
+html_logo = "images/logo_statemodify.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs. This file should be a Windows icon file (.ico), 16x16 or 32x32 pixels.

docs/source/getting-started/quickstarter.rst

@@ -16,7 +16,7 @@ To demonstrate the functionality of **statemodify**, we have generated 5 noteboo
 6. Plot the new shortages or reservoir levels with respect to the baseline values.
 
 
-The notebooks are hosted in MSD-LIVE containers and can be found at: `https:/statemodify.msdlive.org <https:/statemodify.msdlive.org>` 
+The notebooks are hosted in MSD-LIVE containers and can be found at: `https:/statemodify.msdlive.org <https:/statemodify.msdlive.org>`
 
 
 You will be taken to a JupyterLab homepage with "data" and "notebook" buckets on the side.  The "data" directory contains all the StateMod datasets and some other template files. Click on the "notebooks" directory and choose a notebook to start. Press "shift + enter" to execute the cells in the notebook.
@@ -27,15 +27,15 @@ You will be taken to a JupyterLab homepage with "data" and "notebook" buckets on
 
   Figure 1: JupyterLab home screen
 
-IMPORTANT: When you finish a notebook and move on to another one, please restart the kernel and clear the outputs as shown below. 
+IMPORTANT: When you finish a notebook and move on to another one, please restart the kernel and clear the outputs as shown below.
 
 .. figure:: ../images/quickstarter_2.png
-  :alt: Restarting the Kernel 
+  :alt: Restarting the Kernel
 
-  Figure 1: Restarting the Kernel 
+  Figure 1: Restarting the Kernel
 
 
-The table below lists the  
+The table below lists the
 
 .. list-table:: Notebook Topics
    :widths: 25 50 50 50 50 50
@@ -49,8 +49,15 @@ The table below lists the
      - Notebook 5: Sampling multiple uncertainties
 
    * - Description
-     - This notebook has more general intro information on **statemodify** and shows how changes to demand and water rights can lead to changes to user shortages in the San Juan Subbasin. 
+     - This notebook has more general intro information on **statemodify** and shows how changes to demand and water rights can lead to changes to user shortages in the San Juan Subbasin.
      - This notebook looks at how changes in evaporation in  reservoirs in the Gunnison subbasin lead to changes to reservoir levels
-     - This notebook looks at how changes in storage in reservoirs in the Upper Colorado subbasin lead to changes to user shortages 
-     - This notebook debuts the stationary Hidden Markov Model to generate alternative streamflow scenarios across the basins. 
-     - This notebook demonstrates how to create a global Latin hypercube sample to consider multiple uncertainties in a basin. 
+     - This notebook looks at how changes in storage in reservoirs in the Upper Colorado subbasin lead to changes to user shortages
+     - This notebook debuts the stationary Hidden Markov Model to generate alternative streamflow scenarios across the basins.
+     - This notebook demonstrates how to create a global Latin hypercube sample to consider multiple uncertainties in a basin.
+
+
+.. include:: ../notebooks/N1_Demand_WaterRights_File_Modification.rst
+.. include:: ../notebooks/N2_Evaporation_File_Modification.rst
+.. include:: ../notebooks/N3_Reservoir_File_Modification.rst
+.. include:: ../notebooks/N4_Streamflow_File_Modification.rst
+.. include:: ../notebooks/N5_Batch_Modification.rst