Update demo notebook 3

.coveragerc

@@ -0,0 +1,24 @@
+[html]
+directory = coverage
+
+[run]
+source =
+    instageo
+omit =
+    */__init__.py
+    *_test.py
+
+[report]
+omit =
+    __init__.py
+    *_test.py
+    *app.py
+
+exclude_lines =
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

.github/workflows/tests_and_linters.yaml

@@ -0,0 +1,37 @@
+name: Tests and Linters 🧪
+
+on: [push, pull_request]
+
+jobs:
+  tests-and-linters:
+    name: "Python 3.10 on Ubuntu Latest"
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install dependencies for viewer test
+        run: sudo apt-get update && sudo apt-get install -y xvfb
+      - name: Checkout your repo 📦
+        uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install python dependencies 🔧
+        run: |
+          pip install --upgrade pip
+          pip install -r requirements.txt \
+          -r instageo/model/requirements.txt \
+          -r instageo/data/requirements.txt \
+          -r instageo/apps/requirements.txt
+
+      - name: Run linters 🖌️
+        run: pre-commit run --all-files --verbose
+      - name: Set PYTHONPATH
+        run: echo "PYTHONPATH=$PYTHONPATH:$(pwd)" >> $GITHUB_ENV
+      - name: Run tests 🧪
+        env:
+          EARTHDATA_USERNAME: ${{ secrets.EARTHDATA_USERNAME }}
+          EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }}
+        run: pytest --cov --cov-config=.coveragerc --cov-report=html --cov-report=term-missing --cov-fail-under=50 -m "not auth"
+#      - name: Test build docs 📖
+#        run: mkdocs build --verbose --site-dir docs_public

.gitignore

@@ -20,6 +20,7 @@ parts/
 sdist/
 var/
 wheels/
+pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -49,7 +50,6 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -72,7 +72,6 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -83,35 +82,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+.python-version
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
 # Celery stuff
@@ -148,15 +121,26 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# pytype static type analyzer
-.pytype/
+# PyCharm stuff
+.idea/
+
+# VSCode stuff
+.vscode
+
+# Docker stuff
+.devcontainer
 
-# Cython debug symbols
-cython_debug/
+# MacBook Finder
+.DS_Store
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+# Experiment results
+outputs/
+
+
+*.pyc
+__pycache__/
+*lightning_logs
+*prithvi/
+nul/
+notebooks/
+!notebooks/*.ipynb

.pre-commit-config.yaml

@@ -0,0 +1,88 @@
+# Pre-commit hooks for repo.
+
+# Packages:
+#   pre-commit: General pre-commits for formatting.
+#   black: Python code strict formatting.
+#   pyupgrade:  Upgrade syntax for newer versions of the language.
+#   isort: Sorts imports.
+#   flake8: Checks code follows PEP8 standard.
+#   mypy: Static typing.
+#   conventional-pre-commit: commit format checker.
+#   blacken-docs: Checks docs follow black format standard.
+#   pydocstyle: Checking docstring style.
+
+default_stages: ["commit", "commit-msg", "push"]
+default_language_version:
+  python: python3.10
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude_types: [image]
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: mixed-line-ending
+      - id: check-yaml
+
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+        exclude_types: [image]
+        language_version: python3
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        args:
+          [
+            "--max-line-length=100",
+            "--extend-ignore=E203,BLK100",
+            "--exclude=*tests*",
+          ]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.0
+    hooks:
+      - id: mypy
+        exclude: ^docs/|test
+        args: [--config-file=setup.cfg]
+
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v3.0.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black>=22.1.0]
+        language_version: python3
+
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+        name: Checking docstring style.
+        args:
+          [
+            "--convention=google",
+            "--match=^((?!test).)*$",
+          ]

instageo/model/dataloader.py

@@ -123,9 +123,8 @@ def process_and_augment(
     label = None
     # convert to PIL for easier transforms
     ims = [Image.fromarray(im) for im in ims]
-    if not (y is None):
-        label = y.copy()
-        label = Image.fromarray(label.squeeze())
+    if y is not None:
+        label = Image.fromarray(y.copy().squeeze())
     if train:
         ims, label = random_crop_and_flip(ims, label, im_size)
     ims, label = normalize_and_convert_to_tensor(ims, label, mean, std, temporal_size)
@@ -245,8 +244,8 @@ def get_raster_data(
             data = src.read()
     if (not is_label) and bands:
         data = data[bands, ...]
-    # For some reasons, some few HLS tiles are not scaled. In the following lines,
-    # we find and scale them
+    # For some reasons, some few HLS tiles are not scaled in v2.0.
+    # In the following lines, we find and scale them
     bands = []
     for band in data:
         if band.max() > 10:
@@ -342,7 +341,7 @@ def __init__(
         constant_multiplier: float,
         bands: List[int] | None = None,
     ):
-        """Dataset Class for loading and preprocessing Sentinel11Floods dataset.
+        """Dataset Class for loading and preprocessing the dataset.
 
         Args:
             filename (str): Filename of the CSV file containing data paths.

instageo/model/requirements.txt

@@ -5,3 +5,4 @@ einops
 tensorboard
 omegaconf
 hydra-core
+torchvision

instageo/model/run.py

@@ -85,6 +85,23 @@ def get_device() -> str:
     return device
 
 
+def custom_collate_fn(batch: tuple[torch.Tensor]) -> tuple[torch.Tensor, torch.Tensor]:
+    """Test DataLoader Collate Function.
+
+    This function is a convenient wrapper around the PyTorch DataLoader class,
+    allowing for easy setup of various DataLoader parameters.
+
+    Args:
+        batch (Tuple[Tensor]): A list of tuples containing features and labels.
+
+    Returns:
+        Tuple of (x,y) concatenated into separate tensors
+    """
+    data = torch.cat([a[0] for a in batch], 0)
+    labels = torch.cat([a[1] for a in batch], 0)
+    return data, labels
+
+
 def create_dataloader(
     dataset: Dataset,
     batch_size: int,
@@ -522,12 +539,7 @@ def main(cfg: DictConfig) -> None:
             constant_multiplier=cfg.dataloader.constant_multiplier,
         )
         test_loader = create_dataloader(
-            test_dataset,
-            batch_size=batch_size,
-            collate_fn=lambda x: (
-                torch.cat([a[0] for a in x], 0),
-                torch.cat([a[1] for a in x], 0),
-            ),
+            test_dataset, batch_size=batch_size, collate_fn=custom_collate_fn
         )
         model = PrithviSegmentationModule.load_from_checkpoint(
             checkpoint_path,