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Merge pull request #76 from FR-DC/0.1.2
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0.1.2
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@Eve-ning
Eve-ning authored Jun 28, 2024
2 parents df7d1a6 + bcea011 commit 5ababee
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5 changes: 5 additions & 0 deletions .env.example
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LABEL_STUDIO_API_KEY=
LABEL_STUDIO_HOST=10.97.41.70
LABEL_STUDIO_PORT=8080
GCS_PROJECT_ID=frmodel
GCS_BUCKET_NAME=frdc-ds
6 changes: 5 additions & 1 deletion .github/workflows/basic-tests.yml
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Expand Up @@ -6,6 +6,7 @@ on:
pull_request:
paths:
- "src/frdc/**"
- "poetry.lock"

jobs:
build:
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python -m pip install flake8 pytest poetry
poetry export --with dev --without-hashes -o requirements.txt
pip install -r requirements.txt
pip install torch torchaudio torchvision lightning
- name: Lint with flake8
run: |
Expand All @@ -49,6 +49,10 @@ jobs:
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 src/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Copy over .env
run: |
cp .env.example .env
- name: Test with pytest
run: |
pytest
5 changes: 4 additions & 1 deletion .github/workflows/model-tests.yml
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Expand Up @@ -53,7 +53,6 @@ jobs:
python3 -m pip install flake8 pytest poetry
poetry export --with dev --without-hashes -o requirements.txt
pip3 install -r requirements.txt
pip3 install torch torchvision torchaudio
- name: Check CUDA is available
run: nvidia-smi
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uses: mxschmitt/action-tmate@v3
if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}

- name: Copy over .env
run: |
cp .env.example .env
- name: Run Model Training
working-directory: ${{ github.workspace }}/tests
run: |
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2 changes: 1 addition & 1 deletion Writerside/d.tree
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start-page="Overview.md">

<toc-element topic="Overview.md"/>
<toc-element topic="ML-Architecture.md"/>
<toc-element topic="Getting-Started.md">
<toc-element topic="Get-Started-with-Dev-Containers.md"/>
</toc-element>
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<toc-element topic="preprocessing.extract_segments.md"/>
<toc-element topic="preprocessing.morphology.md"/>
<toc-element topic="preprocessing.glcm_padded.md"/>
<toc-element topic="train.frdc_lightning.md"/>
</toc-element>
</instance-profile>
5 changes: 5 additions & 0 deletions Writerside/topics/Get-Started-with-Dev-Containers.md
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Expand Up @@ -47,3 +47,8 @@ steps such as:
- Google Cloud Application Default Credentials
- Weight & Bias API Key
- Label Studio API Key

> You can set the API Keys in the `.env` file in the root of the project.
> Be careful not to commit the `.env` file to the repository, which should
> have been ignored by default.
{style='note'}
274 changes: 147 additions & 127 deletions Writerside/topics/Getting-Started.md
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# Getting Started

> Want to use a Dev Container? See [Get Started with Dev Containers](Get-Started-with-Dev-Containers.md)
> Want to use a Dev Container?
> See [Get Started with Dev Containers](Get-Started-with-Dev-Containers.md)
<procedure title="Installing the Dev. Environment" id="install">
<step>Ensure that you have the right version of Python.
The required Python version can be seen in <code>pyproject.toml</code>
<code-block lang="ini">
[tool.poetry.dependencies]
python = "..."
</code-block>
</step>
<step>Start by cloning our repository.
<code-block lang="shell">
git clone https://github.com/FR-DC/FRDC-ML.git
</code-block>
</step>
<step>Then, create a Python Virtual Env <code>pyvenv</code>
<tabs>
<tab title="Windows">
<code-block lang="shell">python -m venv venv/</code-block>
</tab>
<tab title="Linux">
<code-block lang="shell">python3 -m venv venv/</code-block>
</tab>
</tabs>
</step>
<step>
<a href="https://python-poetry.org/docs/">Install Poetry</a>
Then check if it's installed with
<code-block lang="shell">poetry --version</code-block>
<warning>
If <code>poetry</code> is not found, it's likely not in the user PATH.
</warning>
</step>
<step>Activate the virtual environment
<tabs>
<tab title="Windows">
<code-block lang="shell">
cd venv/Scripts
activate
cd ../..
</code-block>
</tab>
<tab title="Linux">
<code-block lang="shell">
source venv/bin/activate
</code-block>
</tab>
</tabs>
</step>
<step>Install the dependencies. You should be in the same directory as
<code>pyproject.toml</code>
<step>Ensure that you have the right version of Python.
The required Python version can be seen in <code>pyproject.toml</code>
<code-block lang="ini">
[tool.poetry.dependencies]
python = "..."
</code-block>
</step>
<step>Start by cloning our repository.
<code-block lang="shell">
git clone https://github.com/FR-DC/FRDC-ML.git
</code-block>
</step>
<step>Then, create a Python Virtual Env <code>pyvenv</code>
<tabs>
<tab title="Windows">
<code-block lang="shell">python -m venv venv/</code-block>
</tab>
<tab title="Linux">
<code-block lang="shell">python3 -m venv venv/</code-block>
</tab>
</tabs>
</step>
<step>
<a href="https://python-poetry.org/docs/">Install Poetry</a>
Then check if it's installed with
<code-block lang="shell">poetry --version</code-block>
<warning>
If <code>poetry</code> is not found, it's likely not in the user PATH.
</warning>
</step>
<step>Activate the virtual environment
<tabs>
<tab title="Windows">
<code-block lang="shell">
poetry install --with dev
cd venv/Scripts
activate
cd ../..
</code-block>
</step>
<step>Install Pre-Commit Hooks
</tab>
<tab title="Linux">
<code-block lang="shell">
pre-commit install
source venv/bin/activate
</code-block>
</step>
</tab>
</tabs>
</step>
<step>Install the dependencies. You should be in the same directory as
<code>pyproject.toml</code>
<code-block lang="shell">
poetry install --with dev
</code-block>
</step>
<step>
Make a copy of the <code>.env.example</code> file and rename it to
<code>.env</code>
</step>
<step>Fill in additional environment variables in the <code>.env</code> file
<code-block>
LABEL_STUDIO_API_KEY=...
LABEL_STUDIO_HOST=10.97.41.70
LABEL_STUDIO_PORT=8080
GCS_PROJECT_ID=frmodel
GCS_BUCKET_NAME=frdc-ds
</code-block>
</step>
<step>Install Pre-Commit Hooks
<code-block lang="shell">
pre-commit install
</code-block>
</step>
</procedure>


<procedure title="Setting Up Google Cloud" id="gcloud">
<step>
We use Google Cloud to store our datasets. To set up Google Cloud,
<a href="https://cloud.google.com/sdk/docs/install">
install the Google Cloud CLI
</a>
</step>
<step>
Then,
<a href="https://cloud.google.com/sdk/docs/initializing">
authenticate your account
</a>.
<code-block lang="shell">gcloud auth login</code-block>
</step>
<step>
Finally,
<a href="https://cloud.google.com/docs/authentication/provide-credentials-adc">
set up Application Default Credentials (ADC)
</a>.
<code-block lang="shell">gcloud auth application-default login</code-block>
</step>
<step>
To make sure everything is working, <a anchor="tests">run the tests</a>.
</step>
<step>
We use Google Cloud to store our datasets. To set up Google Cloud,
<a href="https://cloud.google.com/sdk/docs/install">
install the Google Cloud CLI
</a>
</step>
<step>
Then,
<a href="https://cloud.google.com/sdk/docs/initializing">
authenticate your account
</a>.
<code-block lang="shell">gcloud auth login</code-block>
</step>
<step>
Finally,
<a href="https://cloud.google.com/docs/authentication/provide-credentials-adc">
set up Application Default Credentials (ADC)
</a>.
<code-block lang="shell">gcloud auth application-default login</code-block>
</step>
<step>
To make sure everything is working, <a anchor="tests">run the tests</a>.
</step>
</procedure>

<procedure title="Setting Up Label Studio" id="ls">
<tip>This is only necessary if any task requires Label Studio annotations</tip>
<step>
We use Label Studio to annotate our datasets.
We won't go through how to install Label Studio, for contributors, it
should be up on <code>localhost:8080</code>.
</step>
<step>
Then, retrieve your own API key from Label Studio.
<a href="http://localhost:8080/user/account"> Go to your account page </a>
and copy the API key. <br/></step>
<step> Set your API key as an environment variable.
<tabs>
<tab title="Windows">
<tip>This is only necessary if any task requires Label Studio annotations</tip>
<step>
We use Label Studio to annotate our datasets.
We won't go through how to install Label Studio, for contributors, it
should be up on <code>localhost:8080</code>.
</step>
<step>
Then, retrieve your own API key from Label Studio.
<a href="http://localhost:8080/user/account"> Go to your account page </a>
and copy the API key. <br/></step>
<step> Set your API key as an environment variable.
<tabs>
<tab title="Windows">
In Windows, go to "Edit environment variables for
your account" and add this as a new environment variable with name
<code>LABEL_STUDIO_API_KEY</code>.
</tab>
<tab title="Linux">
</tab>
<tab title="Linux">
Export it as an environment variable.
<code-block lang="shell">export LABEL_STUDIO_API_KEY=...</code-block>
</tab>
</tabs>
</step>
</tab>
<tab title=".env">
In all cases, you can create a <code>.env</code> file in the root of
the project and add the following line:
<code>LABEL_STUDIO_API_KEY=...</code>
</tab>
</tabs>
</step>
</procedure>

<procedure title="Setting Up Weight and Biases" id="wandb">
<step>
We use W&B to track our experiments. To set up W&B,
<a href="https://docs.wandb.ai/quickstart">
install the W&B CLI
</a>
</step>
<step>
Then,
<a href="https://docs.wandb.ai/quickstart">
authenticate your account
</a>.
<code-block lang="shell">wandb login</code-block>
</step>
<step>
We use W&B to track our experiments. To set up W&B,
<a href="https://docs.wandb.ai/quickstart">
install the W&B CLI
</a>
</step>
<step>
Then,
<a href="https://docs.wandb.ai/quickstart">
authenticate your account
</a>.
<code-block lang="shell">wandb login</code-block>
</step>
</procedure>

<procedure title="Pre-commit Hooks" collapsible="true">
<note>This is optional but recommended.
Pre-commit hooks are a way to ensure that your code is formatted correctly.
This is done by running a series of checks before you commit your code.
</note>
<step>
<code-block lang="shell">
pre-commit install
</code-block>
</step>
<note>This is optional but recommended.
Pre-commit hooks are a way to ensure that your code is formatted correctly.
This is done by running a series of checks before you commit your code.
</note>
<step>
<code-block lang="shell">
pre-commit install
</code-block>
</step>
</procedure>

<procedure title="Running the Tests" id="tests">
<step>
Run the tests to make sure everything is working
<code-block lang="shell">
pytest
</code-block>
</step>
<step>
Run the tests to make sure everything is working
<code-block lang="shell">
pytest
</code-block>
</step>
</procedure>

## Troubleshooting
Expand All @@ -174,13 +192,15 @@ See [Setting Up Google Cloud](#gcloud)
### Couldn't connect to Label Studio

Label Studio must be running locally, exposed on `localhost:8080`. Furthermore,
you need to specify the `LABEL_STUDIO_API_KEY` environment variable. See
you need to specify the `LABEL_STUDIO_API_KEY` environment variable. See
[Setting Up Label Studio](#ls)

### Cannot login to W&B

You need to authenticate your W&B account. See [Setting Up Weight and Biases](#wandb)
If you're facing difficulties, set the `WANDB_MODE` environment variable to `offline`
You need to authenticate your W&B account.
See [Setting Up Weight and Biases](#wandb)
If you're facing difficulties, set the `WANDB_MODE` environment variable
to `offline`
to disable W&B.

## Our Repository Structure
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