Simplified uv venv and dependency install. Fixed a couple links. (#12)

Simplified uv venv and dependency install. Fixed a couple links.

Author: wdar

docs/dev_guide/contribute.md

@@ -13,7 +13,7 @@ This project uses a fork-and-pull-request workflow. You will need to make your [
 2. Clone the repository from  your fork `git clone https://github.com/{your_github_username}/CDIPpy.git` - this will add your own fork as your `origin` remote repo. *Note: If you already have the main fork cloned, skip to the next step and follow instuctions to add your fork as another remote.*
 3. Add the main fork as another remote (or your fork, if you cloned from the main fork). This will allow you to pull latest code from the main fork, but push your own development to your own fork:  
 ```bash
-git add remote cdip https://github.com/{your_github_username}/CDIPpy.git
+git add remote cdip https://github.com/cdipsw/CDIPpy.git
 git fetch cdip
 git remote -v
 ```

docs/dev_guide/index.md

@@ -1,35 +1,35 @@
-# Installing CDIPpy for development 
+# Installing CDIPpy for development
 This page contains instructions for CDIPpy users interested in customizing or contributing to the library.
 
 ## Download source
-Clone the [CDIPpy repository](https://github.com/cdipsw/CDIPpy):  
+Clone the [CDIPpy repository](https://github.com/cdipsw/CDIPpy):
 
 * using `ssh` - `git clone git@github.com:cdipsw/CDIPpy.git`
 * using `https` - `git clone https://github.com/cdipsw/CDIPpy.git`
 
 If you need help getting started with [Git](https://git-scm.com/doc) and [GitHub](https://docs.github.com/en/enterprise-cloud@latest/get-started).
-You'll specifically want to look at configuring credentials with [https](https://git-scm.com/docs/gitcredentials) or [ssh](https://docs.github.com/en/authentication/connecting-to-github-with-ssh).  
-[Oh Shit, Git?!](https://ohshitgit.com/) is another great resource for fixing git problems.
+You'll specifically want to look at configuring credentials with [https](https://git-scm.com/docs/gitcredentials) or [ssh](https://docs.github.com/en/authentication/connecting-to-github-with-ssh).
+
+[Dangit, Git!?!](https://dangitgit.com/) is another great resource for fixing git problems.
 
 ## Install with dev tools
 It is recommended to us [`uv`](https://docs.astral.sh/uv/) to manage you development environment for this project, but other package managers will likely work as well. This documentation provides instructions for using `uv`.
 
 Navigate to the project root dirctory ('CDIPpy/') and run the following:
 ``` bash
->>> pip install uv # install uv pacakge manager
->>> uv venv # create a virtual envionment at CDIPpy/.venv/
->>> source activate .venv/bin/activate # activate the environment
->>> uv pip install -e .[dev] # install the source code, its runtime dependencies, and its dev. dependencies.
+>>> pip install uv  # install uv pacakge manager
+>>> uv sync  # create a virtual envionment at CDIPpy/.venv/, install the source code, its runtime dependencies and it's dev dependencies defined in pyproject.toml.
+>>> source .venv/bin/activate  # activate the environment
 ```
-Using the `-e` flag tells `uv` to point the installation to the source code directory, so that changes you make will be automatically reflected in the environment without reinstalling the package. The `[dev]` specifier installs the packages requires to run tests, lint, and build documentation.
+To exclude the development dpendancies, you can run `uv sync --no-dev`.
 
 ### testing
 You can check that your dev installation was successful by running unit tests from the root directory: `python -m unittest discover`.  
-This runs every test in the library; you should see all successful tests.  
+This runs every test in the library; you should see all successful tests.
 
 Learn more about running specific tests or subsets from the [`unittest` docs](https://docs.python.org/3/library/unittest.html).
 
 ### linting
-This library uses `flake8` to check for adherance to the [PEP8](https://peps.python.org/pep-0008/) style guide. To check whether your code is compliant with the project style, run `flake8 .` from the project root.  You can fix problems manually, or use a tool like [`black`](https://black.readthedocs.io/en/stable/) to autolint: `black .`.  
+This library uses `flake8` to check for adherance to the [PEP8](https://peps.python.org/pep-0008/) style guide. To check whether your code is compliant with the project style, run `flake8 .` from the project root.  You can fix problems manually, or use a tool like [`black`](https://black.readthedocs.io/en/stable/) to autolint: `black .`.
 
 This project also provides a [`pre-commit`](https://pre-commit.com/) hook to manage style for you autmatically on every `git commit`. To install it, run `pre-commit install` from the project root - this will use `black` and `flake` to autolint and check any changes you make for style before committing them to the repository.

docs/quickstart.md

@@ -1,32 +1,31 @@
 ## Installation
 To install CDIPpy locally, you can either  
-1.  clone the repository, navigate to the root directory, and run `pip install .` or   
-2. without cloning the repository, install from github:  
+1. Clone the repository, navigate to the root directory, and run `pip install .` or  
+2. Without cloning the repository, install from github:  
 *https: `pip install git+https://github.com/cdipsw/CDIPpy.git`*  
 *ssh: `pip install git+ssh://github.com/cdipsw/CDIPpy.git`*
 
 {{ under_construction("add test snippet to check installation here") }}
 
 ---
 
-## Development  
-To set up a development copy of CDIPpy, install the project form source using [`uv`](https://docs.astral.sh/uv/):  
+## Development
+To set up a development copy of CDIPpy, install the project form source using [`uv`](https://docs.astral.sh/uv/):
 ``` bash
 >>> pip install uv
->>> uv venv
->>> source activate .venv/bin/activate
->>> uv pip install -e .[dev]
+>>> uv sync
+>>> source .venv/bin/activate
 ```
 
-This creates a local, virtual environment at `./.venv`, and installs a version of CDIPpy that is editable (`-e`), along with several additional dev dependencies (`[dev]`).
+This creates a local, virtual environment at `./.venv` and installs a version of CDIPpy along with several additional `dev` dependencies defined in the pyproject.toml file.
 
 ---
 ### Testing
-This project uses python's built in `unittest` package. To run all tests: 
+This project uses python's built in `unittest` package. To run all tests:
 ~~~ bash
 >>> python -m unittest discover
 ~~~
-To run with [coverage](https://coverage.readthedocs.io/en/7.8.2/):
+To run with [`coverage`](https://coverage.readthedocs.io/en/latest/):
 ~~~ bash
 >>> coverage run -m unittest discover
 ~~~
@@ -45,4 +44,4 @@ Contributions are welcome and should be merged via pull request on the `main` br
 * there must be at least one reviewer approval
 * a CLA must be signed by the contributor, if this is their first commit
 
-If you do not wish you manually check the style for every commit, there is a pre-commit hook that can do it for you. After setting up CDIPpy for development, install the hook with: `pre-commit install`. The installed hook will auto-format the files in your commit with [`black`](https://black.readthedocs.io/en/stable/) and checked for any remaining format errors with `flake8`. 
+If you do not wish you manually check the style for every commit, there is a pre-commit hook that can do it for you. After setting up CDIPpy for development, install the hook with: `pre-commit install`. The installed hook will auto-format the files in your commit with [`black`](https://black.readthedocs.io/en/stable/) and checked for any remaining format errors with `flake8`.

pyproject.toml

@@ -1,5 +1,3 @@
-
-
 [project]
 name = "cdippy"
 version = "0.1.0"
@@ -18,16 +16,6 @@ dependencies = [
 ]
 keywords = ["oceanography", "waves", "buoy", "data"]
 
-[project.optional-dependencies]
-dev = [
-    "black",
-    "coverage",
-    "flake8",
-    "mkdocs",
-    "mkdocs-macros-plugin",
-    "pre-commit"
-]
-
 [project.urls]
 Homepage = "https://cdip.ucsd.edu"
 Source = "https://github.com/cdipsw/CDIPpy"
@@ -38,3 +26,13 @@ packages = ["cdippy"]
 [build-system]
 requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
+
+[dependency-groups]
+dev = [
+    "black",
+    "coverage",
+    "flake8",
+    "mkdocs",
+    "mkdocs-macros-plugin",
+    "pre-commit",
+]