Slan to ImodModel attribute and IMAT to ImodModel.object attribute + testing & documentation

[braxtonowens]

1. I incorrectly made Slicer angles an ImodModel.object attribute in Parse SLAN Chunks #17. It is now an ImodModel attribute.
   IMAT is now an ImodModel.object attribute instead of an ImodModel attribute.

2. Added mod file with multiple objects along with testing.

3. Added documentation for using ImodModel.

[alisterburt]

Wonderful - while we're at it, do you think the attribute should be .slan or .slicer_angles?

I'm fine with either but prefer the aesthetics of slicer_angles - if we go with slicer_angles can we update the selector for annotation type where it's 'slan' too?

Great work as always @braxtonowens !

[alisterburt]

Looks like you have some merge conflicts, you'll have to rebase on main

[braxtonowens]

Yeah, I like slicer_angles better.

[alisterburt]

Perfect! Minor consistency/style things - merging as soon as tests pass, thanks @braxtonowens !

[alisterburt]

@braxtonowens I've given you maintenance powers on the repo - let's still discuss things over PRs with the other but you're doing a great job and should have the ability to move the project forward 🙂

Would you like to trigger the deployment workflow with this new code so that it's available on PyPI?

The deployment workflow is stored here:

imodmodel/.github/workflows/test_and_deploy.yml

Lines 1 to 76 in 5908efc

	name: tests
	on:
	push:
	branches:
	- master
	- main
	tags:
	- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
	pull_request:
	branches:
	- master
	- main
	workflow_dispatch:
	jobs:
	test:
	name: ${{ matrix.platform }} py${{ matrix.python-version }}
	runs-on: ${{ matrix.platform }}
	strategy:
	matrix:
	platform: [ ubuntu-latest ]
	python-version: [
	"3.8",
	"3.9",
	"3.10",
	"3.11",
	]
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: |
	python -m pip install --upgrade pip
	pip install setuptools pytest pipx
	pip install -e .
	pipx install hatch
	- name: Test with pytest
	run: hatch run all:test -v -p no:warnings tests
	env:
	PLATFORM: ${{ matrix.platform }}
	- name: Coverage
	uses: codecov/codecov-action@v1
	deploy:
	# this will run when you have tagged a commit, starting with "v*"
	# and requires that you have put your twine API key in your
	# github secrets (see readme for details)
	needs: [ test ]
	runs-on: ubuntu-latest
	if: contains(github.ref, 'tags')
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: "3.x"
	- name: Install dependencies
	run: |
	python -m pip install --upgrade pip
	pip install -U setuptools setuptools_scm wheel twine build
	- name: Build and publish
	env:
	TWINE_USERNAME: __token__
	TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
	run: |
	git tag
	python -m build
	twine upload dist/*

If you take a look at that workflow you'll see it is trigger when a 'tagged commit' matching 'v*' is pushed to the main branch.
Deploying will look like:

one time things

• making sure your local main branch is in sync with the main branch here
• setting this repository as a remote called 'upstream' (git remote add upstream [email protected]:teamtomo/imodmodel.git)
• making your local main branch track the upstream branch (git branch -u upstream/main)
• adding SSH keys to your github account

deployment workflow

• git checkout main
• git pull
• git tag v0.0.13 -m "v0.0.13" (version number follows semver)
• git push upstream main --follow-tags

Once you do this, you should see things launch in the actions tab of the repository
https://github.com/teamtomo/imodmodel/actions

If you don't want to do this let me know and I'm happy to do it too - only written up in case you would like to learn

[braxtonowens]

Great, I think everything went smooth for v0.0.13. Thanks for the help.

[alisterburt]

Great!!