Release 1.0.2

.github/workflows/docker_pygem.yml

@@ -0,0 +1,64 @@
+name: 'Build bespoke PyGEM Docker container'
+
+on:
+  # Trigger when these files change in an open PR
+  pull_request:
+    paths:
+      - '.github/workflows/docker_pygem.yml'
+      - 'docker/Dockerfile'
+
+  # Trigger when these files change on the master or dev branches
+  push:
+    branches:
+      - master
+      - dev
+    paths:
+      - '.github/workflows/docker_pygem.yml'
+      - 'docker/Dockerfile'
+
+   # Trigger every Saturday at 12AM GMT
+  schedule:
+    - cron: '0 0 * * 6'
+
+  # Manually trigger the workflow
+  workflow_dispatch:
+
+# Stop the workflow if a new one is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  docker:
+    name: 'Build and push Docker container'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: 'Check out the repo'
+        uses: actions/checkout@v4
+
+      - name: 'Set up Docker buildx'
+        uses: docker/setup-buildx-action@v3
+
+      - name: 'Log into GitHub Container Repository'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          logout: true
+
+      - name: 'Build and Push Docker Container'
+        uses: docker/build-push-action@v5
+        with:
+          push: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/dev' }}
+          no-cache: true
+          file: 'docker/Dockerfile'
+          build-args: |
+            PYGEM_BRANCH=${{ github.ref == 'refs/heads/master' && 'master' || 'dev' }}
+          tags: |
+            ghcr.io/pygem-community/pygem:${{ github.ref == 'refs/heads/master' && 'latest' || github.ref == 'refs/heads/dev' && 'dev' }}

.github/workflows/test_suite.yml

@@ -0,0 +1,62 @@
+name: 'Install PyGEM and Run Test Suite'
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+    paths:
+      - '**.py'
+      - '.github/workflows/test_suite.yml'
+      - 'pyproject.toml'
+
+  pull_request:
+    paths:
+      - '**.py'
+      - '.github/workflows/test_suite.yml'
+      - 'pyproject.toml'
+
+  # Run test suite every Saturday at 1AM GMT (1 hour after the Docker image is updated)
+  schedule:
+    - cron: '0 1 * * 6'
+
+# Stop the workflow if a new one is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test_suite:
+    name: 'Test suite'
+    runs-on: ubuntu-latest
+    container:
+      # Use pygem:latest for master branch and pygem:dev otherwise
+      image: ghcr.io/pygem-community/pygem:${{ github.ref == 'refs/heads/master' && 'latest' || 'dev' }}
+      options: --user root
+    env:
+      # Since we are root we need to set PYTHONPATH to be able to find the installed packages
+      PYTHONPATH: /home/ubuntu/.local/lib/python3.12/site-packages
+
+    steps:
+      - name: 'Checkout the PyGEM repo'
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: 'Reinstall PyGEM'
+        run: pip install --break-system-packages -e .
+
+      - name: 'Initialize PyGEM'
+        run: initialize
+
+      - name: 'Clone the PyGEM-notebooks repo'
+        run: |
+          # Use PyGEM-notebook:main for master branch and PyGEM-notebooks:dev otherwise
+          BRANCH=${GITHUB_REF#refs/heads/}
+          git clone --depth 1 --branch $([[ "$BRANCH" == "master" ]] && echo "main" || echo "dev") \
+            https://github.com/pygem-community/PyGEM-notebooks.git
+          echo "PYGEM_NOTEBOOKS_DIRPATH=$(pwd)/PyGEM-notebooks" >> $GITHUB_ENV
+
+      - name: 'Run tests'
+        run: |
+          python3 -m coverage erase
+          python3 -m pytest --cov=pygem -v --durations=20 pygem/tests

README.md

@@ -1,53 +1,10 @@
 ## Python Glacier Evolution Model (PyGEM)
 
-Overview: Python Glacier Evolution Model (PyGEM) is an open-source glacier evolution model coded in Python that models the transient evolution of glaciers. Each glacier is modeled independently using a monthly timestep. PyGEM has a modular framework that allows different schemes to be used for model calibration or model physics (e.g., climatic mass balance, glacier dynamics).
+The Python Glacier Evolution Model (PyGEM) is an open-source glacier evolution model coded in Python that models the transient evolution of glaciers. Each glacier is modeled independently using a monthly timestep. PyGEM has a modular framework that allows different schemes to be used for model calibration or model physics (e.g., climatic mass balance, glacier dynamics).
 
-Manual: Details concerning the model physics, installation, and running the model may be found [here](https://pygem.readthedocs.io/en/latest/).
-
-Usage: PyGEM is meant for large-scale glacier evolution modeling.  PyGEM<1.0.0 are no longer being actively being supported.
-
-***
-
-### Installation
-PyGEM can be downloaded from the Python Package Index ([PyPI](https://pypi.org/project/pygem/)).  We recommend creating a dedicated [Anaconda](https://anaconda.org/) environment to house PyGEM.
-```
-conda create --name <environment_name> python=3.12
-conda activate <environment_name>
-pip install pygem
-```
-This will install all PyGEM dependencies within your conda environment, and set up PyGEM command line tools to run core model scripts.
-
-***
-
-### Setup
-Following installation, an initialization script should to be executed.
-
-The initialization script accomplishes two things:
-1. Initializes the PyGEM configuration file *~/PyGEM/config.yaml*.  If this file already exists, an overwrite prompt will appear.
-2. Downloads and unzips a set of sample data files to *~/PyGEM/*, which can also be manually downloaded [here](https://drive.google.com/file/d/1Wu4ZqpOKxnc4EYhcRHQbwGq95FoOxMfZ/view?usp=drive_link).
-
-Run the initialization script by entering the following in the terminal:
-```
-initialize
-```
-
-***
-
-### Development
-Please report any bugs [here](https://github.com/PyGEM-Community/PyGEM/issues).
-
-If you are interested in contributing to further development of PyGEM, we recommend forking [PyGEM](https://github.com/PyGEM-Community/PyGEM) and then [cloning](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) onto your local machine.
-
-Note, if PyGEM was already installed via PyPI, first uninstall:
-```
-pip uninstall pygem
-````
-
-You can then use pip to install your locally cloned fork of PyGEM in 'editable' mode to easily facilitate development like so:
-```
-pip install -e /path/to/your/cloned/pygem/fork/
-```
+Details concerning the model installation, physics, and more may be found at [pygem.readthedocs.io](https://pygem.readthedocs.io/en/latest/).
 
+PyGEM versions prior to 1.0.0 are no longer actively supported.
 
 ***
 

docker/Dockerfile

@@ -0,0 +1,26 @@
+FROM ubuntu:latest
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    sudo curl vim git tree python3-pip python3-venv python3-dev build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Add non-root user 'ubuntu' to sudo group
+RUN usermod -aG sudo ubuntu && \
+    echo "ubuntu ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/ubuntu
+
+# Switch to non-root user
+USER ubuntu
+WORKDIR /home/ubuntu
+
+# Add .local/bin to PATH
+ENV PATH="/home/ubuntu/.local/bin:${PATH}"
+
+# What PyGEM branch to clone (either master or dev; see docker_pygem.yml)
+ARG PYGEM_BRANCH=master
+
+RUN git clone --branch ${PYGEM_BRANCH} https://github.com/PyGEM-Community/PyGEM.git && \
+    pip install --break-system-packages -e PyGEM
+
+# Clone the PyGEM notebooks repository, which are used for testing
+RUN git clone https://github.com/PyGEM-Community/PyGEM-notebooks.git

docs/contributing.md

@@ -0,0 +1,58 @@
+(contributing_pygem_target)=
+# PyGEM Contribution Guide
+
+Before contributing to PyGEM, it is recommended that you either clone [PyGEM's GitHub repository](https://github.com/PyGEM-Community/PyGEM) directly, or initiate your own fork (as described [here](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)) to then clone.
+
+If PyGEM was already installed in your conda environment (as outlined [here](install_pygem_target)), it is recommended that you first uninstall:
+```
+pip uninstall pygem
+```
+
+Next, clone PyGEM. This will place the code at your current directory, so you may wish to navigate to a desired location in your terminal before cloning:
+```
+git clone https://github.com/PyGEM-Community/PyGEM.git
+```
+If you opted to create your own fork, clone using appropriate repo URL: `git clone https://github.com/YOUR-USERNAME/PyGEM.git`
+
+Navigate to root project directory:
+```
+cd PyGEM
+```
+
+Install PyGEM in 'editable' mode:
+```
+pip install -e .
+```
+
+Installing a package in editable mode creates a symbolic link to your source code directory (*/path/to/your/PyGEM/clone*), rather than copying the package files into the site-packages directory. This allows you to modify the package code without reinstalling it.<br>
+
+## General
+- The `dev` branch is the repository's working branch and should almost always be the base branch for Pull Requests (PRs). Exceptions include hotfixes that need to be pushed to the `master` branch immediately, or updates to the `README`.
+- Do not push to other people's branches. Instead create a new branch and open a PR that merges your new branch into the branch you want to modify.
+
+## Issues
+- Check whether an issue describing your problem already exists [here](https://github.com/PyGEM-Community/PyGEM/issues).
+- Keep issues simple: try to describe only one problem per issue. Open multiple issues or sub-issues when appropriate.
+- Label the issue with the appropriate label (e.g., bug, documentation, etc.).
+- If you start working on an issue, assign it to yourself. There is no need to ask for permission unless someone is already assigned to it.
+
+## Pull requests (PRs)
+- PRs should be submitted [here](https://github.com/PyGEM-Community/PyGEM/pulls).
+- PRs should be linked to issues they address (unless it's a minor fix that doesn't warrant a new issue). Think of Issues like a ticketing system.
+- PRs should generally address only one issue. This helps PRs stay shorter, which in turn makes the review process easier.
+- Concisely describe what your PR does. Avoid repeating what was already said in the issue.
+- Assign the PR to yourself.
+- First, open a Draft PR. Then consider:
+    - Have you finished making changes?
+    - Have you added tests for all new functionalities you introduced?
+    - Have all tests passed in the CI? (Check the progress in the Checks tab of the PR.)
+
+  If the answer to all of the above is "yes", mark the PR as "Ready for review" and request a review from an appropriate reviewer. If in doubt of which reviewer to assign, assign [drounce](https://github.com/drounce).
+- You will not be able to merge into `master` and `dev` branches without a reviewer's approval.
+
+### Reviewing PRs and responding to a review
+- Reviewers should leave comments on appropriate lines. Then:
+  - The original author of the PR should address all comments, specifying what was done and in which commit. For example, a short response like "Fixed in [link to commit]." is often sufficient. 
+  - After responding to a reviewer's comment, do not mark it as resolved.
+  - Once all comments are addressed, request a new review from the same reviewer. The reviewer should then resolve the comments they are satisfied with.
+- After approving someone else's PR, do not merge it. Let the original author of the PR merge it when they are ready, as they might notice necessary last-minute changes.

docs/index.rst

@@ -56,7 +56,7 @@ with respect to modeling glacier dynamics and ice thickness inversions.
    :maxdepth: 1
    :caption: Contributing:
 
-   dev
+   contributing
    citing
 
 .. Indices and tables

docs/install_pygem.md

@@ -1,30 +1,35 @@
 (install_pygem_target)=
-# Installing PyGEM
-The Python Glacier Evolution Model has been packaged using Poetry and is hosted on the Python Package Index ([PyPI](https://pypi.org/project/pygem/)), such that all dependencies should install seamlessly. It is recommended that users create a [Anaconda](https://anaconda.org/) environment from which to install the model dependencies and core code.
+# Installation
+The Python Glacier Evolution Model has been packaged using Poetry and is hosted on the Python Package Index ([PyPI](https://pypi.org/project/pygem/)), to ensure that all dependencies install seamlessly. It is recommended that users create a [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/index.html) environment from which to install the model dependencies and core code. If you do not yet have conda installed, see [conda's documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/install) for instructions.
 
-### Setup Conda Environment
-Anaconda is a Python dependency management tool. An Anaconda (conda) environment is essentially a directory that contains a specific collection of installed packages. The use of environments reduces issues caused by package dependencies. It is recommended that users first create conda environment from which to install PyGEM and its dependencies (if you do not yet have conda installed, see [conda's documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/install) for instructions).  We recommend a conda environment with python >=3.10, <3.13.
+Next, choose your preferred PyGEM installation option:<br>
+- [**stable**](stable_install_target): this is the latest version that has been officially released to PyPI, with a fixed version number (e.g. v1.0.1). It is intended for general use.
+- [**development**](dev_install_target): this is the development version of PyGEM hosted on [GitHub](https://github.com/PyGEM-Community/PyGEM/tree/dev). It might contain new features and bug fixes, but is also likely to continue to change until a new release is made. This is the recommended option if you want to work with the latest changes to the code. Note, this installation options require [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) software to be installed on your computer.
 
-A new conda environment can be created from the command line such as:
-```
-conda create --name <environment_name> python=3.12
-```
+**Copyright note**: PyGEM's installation instructions are modified from that of [OGGM](https://docs.oggm.org/en/stable/installing-oggm.html)
 
-### PyPI installation
-Ensure you've activated your PyGEM environment
-```
-conda activate <environment_name>
+(stable_install_target)=
+## Stable install
+The simplest **stable** installation method is to use an environment file. Right-click and save PyGEM's recommended environment file from [this link](https://github.com/PyGEM-Community/PyGEM/tree/master/docs/pygem_env.yml).
+
+From the folder where you saved the file, run `conda env create -f pygem_environment.yml`.
+```{note}
+By default the environment will be named `pygem`. A different name can be specified in the environment file.
 ```
 
-Next, install PyGEM via [PyPI](https://pypi.org/project/pygem/):
+(dev_install_target)=
+## Development install
+Install the [development version](https://github.com/PyGEM-Community/PyGEM/tree/dev) of PyGEM in your conda environment using pip:
 ```
-pip install pygem
+pip uninstall pygem
+pip install git+https://github.com/PyGEM-Community/pygem/@dev
 ```
 
-This will install all PyGEM dependencies within your conda environment, and set up PyGEM command line tools to run core model scripts.
+If you intend to access and make your own edits to the model's source code, see the [contribution guide](contributing_pygem_target).
 
-### Setup
-Following installation, an initialization script should to be executed.
+(setup_target)=
+# Setup
+Following installation, an initialization script should be executed.
 
 The initialization script accomplishes two things:
 1. Initializes the PyGEM configuration file *~/PyGEM/config.yaml*. If this file already exists, an overwrite prompt will appear.
@@ -35,5 +40,5 @@ Run the initialization script by entering the following in the terminal:
 initialize
 ```
 
-### Demonstration Notebooks
-A series of accompanying Jupyter notebooks have been produces for demonstrating the functionality of PyGEM. These can be acquired and installed from [GitHub](https://github.com/PyGEM-Community/PyGEM-notebooks).
+# Demonstration Notebooks
+A series of accompanying Jupyter notebooks has been produced for demonstrating the functionality of PyGEM. These are hosted in the [PyGEM-notebooks repository](https://github.com/PyGEM-Community/PyGEM-notebooks).

docs/pygem_environment.yml

@@ -0,0 +1,6 @@
+name: pygem
+dependencies:
+  - python>=3.10,<3.13
+  - pip
+  - pip:
+    - pygem

pygem/bin/op/duplicate_gdirs.py

@@ -11,11 +11,11 @@
 import os
 import shutil
 # pygem imports
-import pygem.setup.config as config
-# check for config
-config.ensure_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 
 def main():
     parser = argparse.ArgumentParser(description="Script to make duplicate oggm glacier directories - primarily to avoid corruption if parellelizing runs on a single glacier")