chore: Revert a bunch of commits

.github/config.yml

@@ -5,15 +5,15 @@
 
 # Comment to be posted to on first time issues
 newIssueWelcomeComment: >
-  👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our [contributing guidelines](https://polartoolkit.readthedocs.io/en/latest/contributing.html).
+  👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our [contributing guidelines](https://github.com/mdtanker/polartoolkit/blob/main/docs/contribute.md).
 
 # Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
 
 # Comment to be posted to on PRs from first time contributors in your repository
 newPRWelcomeComment: >
   💖 Thanks for opening this pull request! 💖
 
-  Please make sure you read our [contributing guidelines](https://polartoolkit.readthedocs.io/en/latest/contributing.html).
+  Please make sure you read our [contributing guidelines](https://github.com/mdtanker/polartoolkit/blob/main/docs/contribute.md).
 
   A few things to keep in mind:
 

.github/workflows/ci.yml

@@ -51,7 +51,7 @@ jobs:
       # run all of them to catch failures in different combinations.
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     env:
@@ -73,7 +73,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: polartoolkit
-          environment-file: env/testing_env.yml
+          environment-file: env/test_env.yml
           python-version: ${{ matrix.python-version }}
           channels: conda-forge,nodefaults
           channel-priority: strict
@@ -83,18 +83,18 @@ jobs:
           use-mamba: true
           auto-activate-base: false
 
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: mamba list
+
       # Install the package in editable mode
       - name: Install local package
         run: pip install -e .
 
-        # Show installed pkg information for postmortem diagnostic
-      - name: List installed packages
-        run: mamba list
-
       - name: Run the tests
         run: >-
           pytest -m "not earthdata and not issue" -ra --cov --cov-report=xml
           --cov-report=term --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v4.1.0
+        uses: codecov/codecov-action@v4.0.1

.github/workflows/semantic_release.yml

@@ -46,8 +46,6 @@ jobs:
         with:
           fetch-depth: 0
           token: ${{secrets.PAT}}
-      - name: git pull
-        run: git pull origin main --rebase
 
       # use semantic-release
       - id: semantic-release

.pre-commit-config.yaml

@@ -16,14 +16,10 @@ exclude: |
       .github/ISSUE_TEMPLATE/bug_report.md|
       .github/ISSUE_TEMPLATE/feature_request.md|
       .github/config.yml|
-      CONTRIBUTING.md|
+      .github/CONTRIBUTING.md|
       binder/environment.yml|
-<<<<<<< HEAD
       paper/paper.bib|
       paper/paper.md|
-=======
-      templates/CHANGELOG.md.j2|
->>>>>>> 3fffd15 (chore: add ignores to pre-commit)
   )$
 
 repos:

CHANGELOG.md

@@ -2,34 +2,10 @@
 Automatically updated by
 [python-semantic-release](https://python-semantic-release.readthedocs.io/en/latest/)
 with commit parsing of [angular commits](https://github.com/angular/angular.js/blob/master/DEVELOPERS.md#commits).
-
 ## Unreleased
-### 📦️ Build
-### 🧰 Chores / Maintenance
-* fix semantic release action ([`6b12799`](https://github.com/mdtanker/polartoolkit/commit/6b12799d984917e9e4693bf8003c6869fc7f350d))
 
-
-## v0.3.1 (2024-02-22)
-### 📦️ Build
-* extend support to python 3.12 ([`f68def9`](https://github.com/mdtanker/polartoolkit/commit/f68def9b1156f020d4e222bf27279293eddda51f))
-### 🧰 Chores / Maintenance
-* remove shen-2018 hash ([`fbefe40`](https://github.com/mdtanker/polartoolkit/commit/fbefe4031c2b241fdde5b6375bc16b504ec6b9ac))
-* fix test ghf ([`c7c66f6`](https://github.com/mdtanker/polartoolkit/commit/c7c66f60fce00b50524abc6eca01238f40b932e1))
-* update changelog template ([`e4bd1d9`](https://github.com/mdtanker/polartoolkit/commit/e4bd1d923fb635ac2c9724a9c8babbe3cd9a4660))
-* reduce sig figs for test_ghf ([`393aadc`](https://github.com/mdtanker/polartoolkit/commit/393aadc4394bc0da73d4eb38e1318bc04f374636))
-* list packages after installing local for test GHA ([`51250b4`](https://github.com/mdtanker/polartoolkit/commit/51250b4dfa2a8c59380fe16d5f00e68edf453e2d))
-* update testing_env and add make command ([`4ee6945`](https://github.com/mdtanker/polartoolkit/commit/4ee6945f06c39447a6447f3563898c867696fb5c))
-* add hashes to all fetch calls ([`91eb9a8`](https://github.com/mdtanker/polartoolkit/commit/91eb9a83fcdd247b7a55491b0654ae5734c46fed))
-* move contributing file ([`05dff10`](https://github.com/mdtanker/polartoolkit/commit/05dff10fb72fa82a4e24ecf6e47a73d40cdc9c63))
-* add test_fetch make command ([`2a0adb3`](https://github.com/mdtanker/polartoolkit/commit/2a0adb30cdc669b602d6b0f5cdc402b3f5306872))
-* add ignores to pre-commit ([`3fffd15`](https://github.com/mdtanker/polartoolkit/commit/3fffd15defb6de572e2f8caa1e0380a760ac74dd))
-* fix changelog template spacing ([`cabc14a`](https://github.com/mdtanker/polartoolkit/commit/cabc14a644d10bf7eafe26c223a5542e17f10bf4))
 ### 📖 Documentation
-* update install instructions ([`70faf04`](https://github.com/mdtanker/polartoolkit/commit/70faf0485d1157dda42e3f40ca462d89d87fafad))
 * fix links to contrib guide ([`5c6af8d`](https://github.com/mdtanker/polartoolkit/commit/5c6af8de8ab984fa645f868ba23eadd492f0d4b7))
-### 🐛 Bug Fixes
-* increase timeout for shen-2018 moho fetch ([`8d9e183`](https://github.com/mdtanker/polartoolkit/commit/8d9e183de4aca1cc985a4824414b3107c50905e6))
-* delete tmp.nc file in fetch call ([`ee16bdc`](https://github.com/mdtanker/polartoolkit/commit/ee16bdc10f000d1d05cabc889890548fd2f72dbe))
 
 ## v0.3.0 (2024-02-18)
 ### 📦️ Build
@@ -74,7 +50,6 @@ with commit parsing of [angular commits](https://github.com/angular/angular.js/b
 * formatting ([`0b294a1`](https://github.com/mdtanker/polartoolkit/commit/0b294a18d71d909bcbbd398dc0634b548faf7165))
 * fix style errors ([`639ba42`](https://github.com/mdtanker/polartoolkit/commit/639ba42c996db46125b5889e5ae35e09217296d7))
 * fix indent ([`efee6d7`](https://github.com/mdtanker/polartoolkit/commit/efee6d702e7db92b5f32d4136be2b0b18eeaf54a))
-
 ## v0.2.1 (2024-01-29)
 ### 📦️ Build
 * add antarctic_plots package for import warning ([`bb4c134`](https://github.com/mdtanker/polartoolkit/commit/bb4c134b6e78377d426781ef1f601a5ba171000b))
@@ -92,9 +67,8 @@ with commit parsing of [angular commits](https://github.com/angular/angular.js/b
 * spelling and formatting ([`a7347ba`](https://github.com/mdtanker/polartoolkit/commit/a7347ba6ca94185414ac3d0a0eec1bb1ef095bfb))
 * spelling  mistakes ([`4c29294`](https://github.com/mdtanker/polartoolkit/commit/4c2929402b66903b2ddc0688333b932c44bba978))
 *  ignore binder env file in pre-commit ([`9aa1c30`](https://github.com/mdtanker/polartoolkit/commit/9aa1c309352965131c40b3d88c4e16afbcdf48a6))
-
 ## v0.2.0 (2024-01-26)
-### 💥 Breaking Changes
+### Other
 * force a major version bump.
 
 BREAKING CHANGE: ([`cc2ecda`](https://github.com/mdtanker/polartoolkit/commit/cc2ecdaae48b4300ae6d41485076273fa612ce64))
@@ -113,7 +87,6 @@ BREAKING CHANGE: ([`cc2ecda`](https://github.com/mdtanker/polartoolkit/commit/cc
 * fix changelog template ([`31083e3`](https://github.com/mdtanker/polartoolkit/commit/31083e3d729cd4fb17f2149665610c5ba7fcd2c0))
 ### ✏️ Formatting
 * formatting ([`d15fe92`](https://github.com/mdtanker/polartoolkit/commit/d15fe924d6097c64b410e4a0802b63774e17074e))
-
 ## v0.1.0 (2023-12-10)
 ### 📦️ Build
 * fix path to docs ([`4bbbd96`](https://github.com/mdtanker/polartoolkit/commit/4bbbd9639a75a50305e28c8102afdda58b774534))
@@ -239,14 +212,21 @@ increments filename variabls since they change type, and standardizes the format
 * formatting ([`f9f82f8`](https://github.com/mdtanker/polartoolkit/commit/f9f82f8201e08212e61c431a9259075884f1b4c5))
 ### Other
 *  ([`90302ba`](https://github.com/mdtanker/polartoolkit/commit/90302ba4e059c6688dad9468c42cb38c62ad6540))
+
 *  ([`12a5299`](https://github.com/mdtanker/polartoolkit/commit/12a5299d590c3ce16e797fd3efd18ea8e7b2234c))
+
 *  ([`c962e56`](https://github.com/mdtanker/polartoolkit/commit/c962e56ca0eca300b9f45bd4104861cd9fdf67dd))
+
 *  ([`95ad63c`](https://github.com/mdtanker/polartoolkit/commit/95ad63c9af3c9b305fdbc97c984ac6bee952c3bf))
+
 *  ([`30ea5aa`](https://github.com/mdtanker/polartoolkit/commit/30ea5aaea6cf599299e0cc7253eaf136b1e54a59))
+
 *  ([`d8c821e`](https://github.com/mdtanker/polartoolkit/commit/d8c821ee79f146bc74171ae358a331815ba1ac7d))
+
 *  ([`f1249f0`](https://github.com/mdtanker/polartoolkit/commit/f1249f0d7cb848f489bd25f8364d1693e704f886))
 
 
+
 > **Note:**
 >🚨
 Everything above this point was generated automatically by Python Semantic Release.

Makefile

@@ -20,9 +20,6 @@ remove:
 test:
 	pytest -m "not earthdata and not issue and not fetch"
 
-test_fetch:
-	pytest -s -m fetch #-rp
-
 format:
 	ruff format $(STYLE_CHECK_FILES)
 
@@ -81,13 +78,3 @@ RTD_env:
 	sed -i '$$d' env/RTD_env.yml
 	# add pip and install local package
 	sed -i '$$a\  - pip\n  - pip:\n    - ../.[docs]' env/RTD_env.yml
-
-# create testing yml
-testing_env:
-	mamba remove --name testing_env --all --yes
-	mamba create --name testing_env --yes --force pygmt
-	mamba env export --name testing_env --no-builds --from-history > env/testing_env.yml
-	# delete last line
-	sed -i '$$d' env/testing_env.yml
-	# add pip and install local package
-	sed -i '$$a\  - pip\n  - pip:\n    - ../.[test]' env/testing_env.yml

docs/contributing.md

@@ -1,3 +1,3 @@
-```{include} ../CONTRIBUTING.md
+```{include} ../.github/CONTRIBUTING.md
 
 ```

docs/install.md

@@ -10,60 +10,39 @@ gives full access the the package in an online environment.
 This Binder environment can also be accessed by clicking the Binder icon in any
 of the `gallery` or `tutorial` examples.
 
-## Install Python
-
-Before installing _PolarToolkit_, ensure you have Python downloaded. If you
-don't, I recommend setting up Python with Miniforge. See the install
-instructions [here](https://github.com/conda-forge/miniforge).
-
-## Install _PolarToolkit_ Locally
-
-There are 3 main ways to install `polartoolkit`. We show them here in order of
-simplest to hardest.
+## Install package
 
 ### Conda / Mamba
 
 The easiest way to install this package and it's dependencies is with conda or
 mamba into a new virtual environment:
 
-```
-mamba create --name polartoolkit --yes --force polartoolkit
-```
+    mamba create --name polartoolkit --yes --force polartoolkit
 
 Activate the environment:
 
-```
-conda activate polartoolkit
-```
+    conda activate polartoolkit
 
 ### Pip
 
-Instead, you can use pip to install `polartoolkit`, but first you need to
-install a few dependencies with conda. This is because `PyGMT` `GeoPandas`, and
+Instead, you can use pip to install polartoolkit, but first you need to install
+a few dependencies with conda. This is because `PyGMT` `GeoPandas`, and
 `Cartopy` all rely on C packages, which can only be install with conda/mamba and
-not with pip.
-
-```{note}
-`conda` and `mamba` are interchangeable
-```
+not with pip. ere I use mamba, but conda will work as well, just replace any
+`mamba` with `conda`:
 
 Create a new virtual environment:
 
-```
-mamba create --name polartoolkit --yes --force pygmt geopandas cartopy
-```
+    mamba create --name polartoolkit --yes --force pygmt geopandas cartopy
 
-activate the environment and use `pip` to install `polartoolkit`:
+Pip install polartoolkit
 
-```
-mamba activate polartoolkit
-pip install polartoolkit
-```
+    mamba activate polartoolkit
+    pip install polartoolkit
 
-```{note}
-to install the optional dependencies, use this instead:
-`pip install polartoolkit[all]`
-```
+If you don't have Python set up on your computer, I recommend setting up python
+with Miniconda. See the install instructions
+[here](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
 
 ### Development version
 

env/test_env.yml

@@ -0,0 +1,52 @@
+# Requirements for running the GitHub Action: test
+# only need run-time dependencies
+name: polartoolkit
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.9
+  - pip
+  # Run-time
+  - pandas
+  - openpyxl
+  - pooch
+  - tqdm
+  - verde>=1.8.0
+  - xarray
+  - netcdf4
+  - h5netcdf
+  - harmonica>=0.6.0
+  - pyproj
+  - matplotlib
+  - pyogrio
+  - rioxarray
+  - scipy
+  - numpy
+  - pygmt
+  - geopandas
+  - zarr
+  - python-dotenv
+  - nptyping
+  # interavtive
+  - geoviews
+  - cartopy
+  - ipyleaflet
+  - ipython
+  # viz
+  - seaborn
+  # test
+  - pytest>=6
+  - pytest-cov>=3
+  - deepdiff
+  # docs
+  - sphinx>=4.0
+  - myst-parser
+  - sphinx-copybutton
+  - sphinx-autodoc-typehints
+  - sphinx-book-theme>=0.3
+  - sphinx-design
+  - nbsphinx
+  - nbconvert
+  - pip:
+    - ../.

paper/paper.md

@@ -65,12 +65,12 @@ Additionally, `PolarToolkit` provides an easy means for exploring datasets with
 
 # Statement of need
 <!-- clearly illustrates the research purpose of the software and places it in the context of related work. -->
-A common workflow for a geospatial scientist might be: navigate to an online repository and download a dataset, place this downloaded file in a local folder on their computer, perform some preprocessing steps, such a re-projecting, or interpolating the data, possibly using tools like GMT [@wesselgeneric2019], perform their scientific analysis on the data, and then create a map with this data using a graphical user interface (GUI) application such as QGIS [@qgisdevelopmentteamqgis2024].
+A common workflow for a geospatial scientist might be; navigate to a online repository and download a dataset, place this downloaded file in a local folder on their computer, perform some preprocessing steps, such a re-projecting, or interpolating the data, possibly using tools like GMT [@wesselgeneric2019], perform their scientific analysis on the data, and then create a map with this data using a graphical user interface (GUI) application such as QGIS [@qgisdevelopmentteamqgis2024].
 These workflows typically require many separate tools (i.e. internet browser, file browser, spatial analysis software, and mapping software), and are often manually repeated many times throughout a manuscript revision process, and throughout the career of the scientist.
 
 `PolarToolkit` aims to consolidate this workflow to be entirely contained within Python, making it both easier and faster to perform all these steps.
-Scripting workflows like this has several advantages: 1) it decreases the chance of human errors, for example using an old-version of the downloaded data or accidentally altering a pre-processing steps, such as referencing a raster of elevation data to the geoid instead of the ellipsoid, and 2) it allows entire workflows to be shared easily between collaborators with a single python file or Jupyter Notebook.
-Although a popular and well-designed similar package exists [Antarctic Mapping Tools, @greeneantarctic2017], PolarToolkit is unique in its open-access without the need for a paid MatLab license.
+Scripting workflows like this has several advantages; 1) it decreases the chance of human errors, for example using an old-version of the downloaded data or accidentally altering a pre-processing steps, such as referencing a raster of elevation data to the geoid instead of the ellipsoid, and 2) it allows entire workflows to be shared easily between collaborators with a single python file or Jupyter Notebook.
+Although a popular and well-designed similar package exists [Antarctic Mapping Tools, @greeneantarctic2017], PolarToolkit is unique in it's open-access without the need for a paid MatLab license.
 
 Written in easy-to-learn Python, and utilizing common geospatial data structures, `PolarToolkit` is designed to be familiar to use for experienced Python users, while also being approachable for beginner coders.
 It is built upon several open-source packages, such a [Pooch](https://www.fatiando.org/pooch/latest/) for data downloading [@uiedapooch2020], [PyGMT](https://www.pygmt.org/latest/) for creating figures [@uiedapygmt2021], and [xarray](https://docs.xarray.dev/en/stable/) and [verde](https://www.fatiando.org/verde/latest/) for geospatial data processing [@hoyerxarray2017; @uiedaverde2018].
@@ -285,4 +285,4 @@ fig.show()
 |fig.show()                            |                         |
 |```                                   |                         |
 +--------------------------------------+-------------------------+
--->
+-->

pyproject.toml

@@ -24,11 +24,10 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
     "Typing :: Typed",
 ]
 readme = "README.md"
-version = "0.3.1"
+version = "0.3.0"
 license = {file = "LICENSE"}
 
 keywords = ["cryosphere", "antarctica", "arctic", "greenland", "maps", "plotting", "pygmt", "cross-section"]

src/polartoolkit/__init__.py

@@ -9,4 +9,4 @@
 
 from __future__ import annotations
 
-__version__ = "0.3.1"
+__version__ = "0.3.0"