Merge branch 'feat-logger/1-remove-stdout-suppression' into feat-logg…

…er/2-replace-print-logger-analysis_db

# Conflicts:
#	src/icesat2waves/analysis_db/A02c_IOWAGA_thredds_prior.py
#	src/icesat2waves/analysis_db/B02_make_spectra_gFT.py
#	src/icesat2waves/analysis_db/B03_plot_spectra_ov.py
#	src/icesat2waves/analysis_db/B06_correct_separate_var.py

.devcontainer/Dockerfile

@@ -0,0 +1,26 @@
+# Use the official Python 3.11 image from the Docker Hub
+FROM python:3.11
+
+# Update the system and install the packages
+RUN apt-get update && apt-get install -y \
+    git-lfs \
+    openmpi-bin \
+    openmpi-doc \
+    libopenmpi-dev \
+    gdal-bin \
+    libgdal-dev
+
+
+# Set the working directory to /app
+WORKDIR /app
+
+# Copy the current directory contents into the container at /app
+COPY . /app
+
+# Create the output directory
+RUN mkdir -p /app/output
+
+# Install any needed packages specified in pyproject.toml
+RUN pip install --editable ".[dev]"
+
+CMD ["/bin/bash"]

.devcontainer/devcontainer.json

@@ -0,0 +1,26 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
+{
+	"name": "Existing Dockerfile",
+	"build": {
+		// Sets the run context to one level up instead of the .devcontainer folder.
+		"context": "..",
+		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+		"dockerfile": "Dockerfile"
+	}
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Uncomment the next line to run commands after the container is created.
+	// "postCreateCommand": "cat /etc/os-release",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "devcontainer"
+}

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every month
+      interval: "monthly"

.github/workflows/publish_pypi.yml

@@ -1,4 +1,4 @@
-name: Publish Icesat2 to PyPI
+name: Publish icesat2waves to PyPI
 
 on:    
   release:
@@ -13,10 +13,10 @@ jobs:
         id-token: write
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.11
 
@@ -32,5 +32,4 @@ jobs:
     - name: Publish to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        packages_dir: dist
-        repository-url: https://test.pypi.org/legacy/
+        packages_dir: dist

.github/workflows/python_ci.yml

@@ -15,9 +15,9 @@ jobs:
       - name: install mpi macos
         if: matrix.os == 'macos-latest'
         run: brew install open-mpi
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.version }} # install the python version needed
           cache: "pip"

.github/workflows/test_icesat2_tracks_pipeline.yml

@@ -13,9 +13,9 @@ jobs:
     steps:
       - name: install mpi
         run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.version }} # install the python version needed
           cache: "pip"

.github/workflows/test_test_suite.yml

@@ -13,11 +13,11 @@ jobs:
     steps:
       - name: install mpi
         run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.version }} # install the python version needed
           cache: "pip"

README.md

@@ -1,10 +1,15 @@
 # ICESAT2 Track Analysis
 
+- [ICESAT2 Track Analysis](#icesat2-track-analysis)
+  - [Installation for Developers](#installation-for-developers)
+  - [Command line interface](#command-line-interface)
+  - [Sample workflow](#sample-workflow)
+
 ## Installation for Developers
 
 Prerequisites:
 - A POSIX-compatible system (Linux or macOS)
-- Python 3.9 (run `python --version` to check that your version of python is correct)
+- Python 3.10 (run `python --version` to check that your version of python is correct)
 - MPI (e.g. from `brew install open-mpi` on macOS)
 - HDF5 (e.g. from `brew install hdf5` on macOS)
 
@@ -50,162 +55,11 @@ Installation:
   > pip install --upgrade --editable ".[dev]"
   > ```
 
-- Check the module `icesat2_tracks` is available by loading the module:
+- Check the module `icesat2waves` is available by loading the module:
   ```shell
-  python -c "import icesat2_tracks; print(icesat2_tracks.__version__)"
+  python -c "import icesat2waves; print(icesat2waves.__version__)"
   ```
 
-## Installing on Oscar (Deprecated)
-
-If any of these commands fail, check the conda configuration (listed below) before retrying for possible fixes.
-
-Load a conda module.
-
-```shell
-module load miniconda/23.1.0
-```
-
-Follow any prompts from the module load command, like running the following line:
-```shell
-source /gpfs/runtime/opt/miniconda/23.1.0/etc/profile.d/conda.sh
-```
-
-Create a new environment using:
-```shell
-conda create --name "2021-icesat2-tracks"
-```
-
-Activate the environment using:
-```shell
-conda activate "2021-icesat2-tracks"
-```
-
-Install or update the packages in the environment with those listed in the `environment.yml` file using:
-```shell
-conda env update --file environment.yml
-```
-
-(You can create and install dependencies in the environment in a single command using:
-```shell
-conda env create --name "2021-icesat2-tracks" --file environment.yml
-```
-... but this has more steps and is thus more likely to fail. Since the installation step takes a long period of time, it is recommended to use the separate commands instead.)
-
-## Conda Configuration (Deprecated)
-
-Conda draws its configuration from multiple places, and will behave differently when the configuration is different, even when using the same `environment.yml` file.
-
-#### `.condarc`
-
-The `.condarc` file in your home directory sets your conda configuration. If the file doesn't exist, you can create it with:
-```shell
-touch ~/.condarc
-```
-
-#### `pkgs_dirs`
-
-`pkgs_dirs` is the location where conda downloads package files from registries like `anaconda.org`. 
-
-If you use the defaults, when trying to install packages you may get a warning like:
-```
-WARNING conda.lock:touch(51): Failed to create lock, do not run conda in parallel processes [errno 13]
-...
-ERROR   Could not open file /gpfs/runtime/opt/miniconda/4.12.0/pkgs/cache/b63425f9.json
-```
-
-In this case, you might be trying to download packages to the global directory `/gpfs/runtime/opt/miniconda/4.12.0/pkgs` where you have no write-permissions, rather than your home directory where you have write-permissions.
-
-View the conda configuration:
-```shell
-conda config --show
-```
-
-Check that the `pkgs_dirs` setting points to a location in your home directory:
-```yaml
-pkgs_dirs:
-  - /users/username/anaconda/pkg
-```
-
-If it doesn't, update this using:
-```shell
-conda config --add pkgs_dirs ~/anaconda/pkg
-```
-
-(Use `--remove` instead of `--add` to remove an entry.)
-
-#### `envs_dirs`
-
-`envs_dirs` is the location where there is a separate directory per environment containing the installed packages.
-
-View the conda configuration:
-```shell
-conda config --show
-```
-
-Check that the `envs_dirs` setting to a location in your home directory:
-```yaml
-envs_dirs:
-  - /users/username/anaconda/envs
-```
-
-... and update this using:
-```shell
-conda config --add envs_dirs ~/anaconda/envs
-```
-
-(Use `--remove` instead of `--add` to remove an entry.)
-
-Always re-check the configuration after running the `conda config` command. 
-
-#### Environment Variables
-
-Note that modules (like `miniconda/23.1.0`) set environment variables like `CONDA_ENVS_PATH` which override the conda config. 
-
-You might view the conda config and see the following entries:
-```yaml
-envs_dirs:
-  - /users/username/anaconda
-  - /users/username/anaconda/envs
-```
-
-If you try to run 
-```shell
-conda config --remove envs_dirs ~/anaconda
-```
-... you'll get a warning:
-```
-'envs_dirs': '/users/username/anaconda' is not in the 'envs_dirs' key of the config file
-```
-
-... and find that the value is still there when you rerun `conda config --show`:
-```yaml
-envs_dirs:
-  - /users/username/anaconda     # <-- still here!
-  - /users/username/anaconda/envs
-```
-
-The value might have been silently set by the `module load` command using an environment variable. 
-
-Check for environment variables by running:
-```shell
-$ printenv | grep ^CONDA_
-CONDA_SHLVL=0
-CONDA_EXE=/gpfs/runtime/opt/miniconda/23.1.0/bin/conda
-CONDA_ENVS_PATH=~/anaconda  # <- this is the offending variable
-CONDA_PYTHON_EXE=/gpfs/runtime/opt/miniconda/23.1.0/bin/python
-```
-
-To unset a value like `CONDA_ENVS_PATH` use:
-```shell
-unset CONDA_ENVS_PATH
-```
-
-... then check that rerun `conda config --show` no longer shows the has modified the conda config to match the values you wanted:
-```yaml
-envs_dirs:
-  - /users/username/anaconda/envs
-```
-
 ## Command line interface
 
 The `icesat2waves` package comes with a command-line interface (CLI) that facilitates interaction with the package directly from your terminal. This can be particularly useful for scripting and automation. You can access the help documentation for the CLI by running the following command: