MNT: migrate package layout from flat to src

.codecov.yml

@@ -7,4 +7,4 @@ coverage:
 
 ignore:
   - tests/*
-  - vip_hci/vip_ds9.py
+  - src/vip_hci/vip_ds9.py

.flake8

@@ -36,4 +36,4 @@ ignore =
     I002,
 
 exclude=
-    vip_hci/objects
+    src/vip_hci/objects

.github/workflows/ci.yml

@@ -43,19 +43,10 @@ jobs:
 #        pre-commit install-hooks
 #        pre-commit install
 #        # Run pre-commit hooks
-#        pre-commit run --files vip_hci/config/*.py
-#	 pre-commit run --files vip_hci/fits/*.py
-#	 pre-commit run --files vip_hci/fm/*.py
-#	 pre-commit run --files vip_hci/greedy/*.py
-#	 pre-commit run --files vip_hci/invprob/*.py
-#	 pre-commit run --files vip_hci/metrics/*.py
-#        pre-commit run --files vip_hci/preproc/*.py
-#        pre-commit run --files vip_hci/psfsub/*.py
-#        pre-commit run --files vip_hci/stats/*.py
-#        pre-commit run --files vip_hci/var/*.py
+#        pre-commit run --files src/**/*.py
     - name: Test with pytest
       run: |
-        pytest tests/pre_3_10 --cov=vip_hci/ --cov-report=xml --splits 3 --group ${{ matrix.group }}
+        pytest tests/pre_3_10 --cov=src --cov-report=xml --splits 3 --group ${{ matrix.group }}
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
 
@@ -87,9 +78,9 @@ jobs:
 #        pre-commit install-hooks
 #        pre-commit install
 #        # Run pre-commit hooks
-#        pre-commit run --files vip_hci/objects/*.py
+#        pre-commit run --files src/vip_hci/objects/*.py
     - name: Test with pytest
       run: |
-        pytest tests/post_3_10 --cov=vip_hci/objects/ --cov-report=xml
+        pytest tests/post_3_10 --cov=src/vpi_hci/objects/ --cov-report=xml
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3

Makefile

@@ -32,13 +32,13 @@ docs:
 	rm -f docs/source/vip_hci.stats.rst
 	rm -f docs/source/vip_hci.var.rst
 	rm -f docs/source/vip_hci.vip_ds9.rst
-	sphinx-apidoc -o docs/source vip_hci
+	sphinx-apidoc -o docs/source src/vip_hci
 	cd docs/source/
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 
 coverage:
-	coverage run --source=vip_hci -m pytest
+	coverage run --source=src -m pytest
 	coverage report -m
 
 test:
@@ -48,18 +48,8 @@ test:
 	pre-commit install --hook-type post-rewrite
 	pre-commit install-hooks
 	pre-commit install
-	pre-commit run --files vip_hci/config/*.py
-	pre-commit run --files vip_hci/fits/*.py
-	pre-commit run --files vip_hci/fm/*.py
-	pre-commit run --files vip_hci/greedy/*.py
-	pre-commit run --files vip_hci/invprob/*.py
-	pre-commit run --files vip_hci/metrics/*.py
-	pre-commit run --files vip_hci/preproc/*.py
-	pre-commit run --files vip_hci/psfsub/*.py
-	pre-commit run --files vip_hci/stats/*.py
-	pre-commit run --files vip_hci/var/*.py
-	pre-commit run --files vip_hci/objects/*.py
-	pytest --cov=vip_hci/ --cov-report=xml
+	pre-commit run --files src/**/*.py
+	pytest --cov=src --cov-report=xml
 	rm confi_hist.pdf
 	rm confi_hist_gaussfit.pdf
 	rm confidence.txt
@@ -68,8 +58,7 @@ test:
 	rm -rf results/
 
 pep8-format:
-	autopep8 --in-place --aggressive vip_hci/*.py
-	autopep8 --in-place --aggressive vip_hci/*/*.py
+	autopep8 --in-place --aggressive src/**/*.py
 	autopep8 --in-place --aggressive tests/*.py
 
 clean:

docs/source/conf.py

@@ -24,7 +24,7 @@
 matplotlib.use("agg")
 
 
-sys.path.insert(0, os.path.abspath('../../vip_hci/'))
+sys.path.insert(0, os.path.abspath('../../src/vip_hci/'))
 
 version = md_version('vip_hci')
 

pyproject.toml

@@ -69,4 +69,4 @@ dev = [
 
 [tool.setuptools]
 zip-safe = false
-packages.find = { namespaces = false }
+packages.find = { where = ["src"], namespaces = false }

src/vip_hci/__init__.py

@@ -0,0 +1,18 @@
+from . import preproc
+from . import config
+from . import fits
+from . import invprob
+from . import psfsub
+from . import fm
+from . import metrics
+from . import stats
+from . import var
+from . import objects
+from .vip_ds9 import *
+
+
+def __getattr__(name: str):
+    if name == '__version__':
+        from importlib.metadata import version
+        return version('vip_hci')
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

vip_hci/config/utils_conf.py → src/vip_hci/config/utils_conf.py

@@ -12,6 +12,7 @@
 import numpy as np
 
 import itertools as itt
+from importlib.metadata import version
 from inspect import signature, Parameter
 from functools import wraps
 import multiprocessing
@@ -43,8 +44,6 @@ def save(self, filename):
 
 
         """
-        from vip_hci import __version__ # TODO: replace this with importlib.metadata.version
-
         vip_object = self.__class__.__name__
 
         if hasattr(self, "_saved_attributes"):
@@ -60,7 +59,7 @@ def save(self, filename):
                         data["_item_{}".format(a)] = True
 
                 np.savez_compressed(
-                    filename, _vip_version=__version__, _vip_object=vip_object, **data
+                    filename, _vip_version=version('vip_hci'), _vip_object=vip_object, **data
                 )
 
         else:
@@ -70,8 +69,6 @@ def save(self, filename):
 
     @classmethod
     def load(cls, filename):
-        from vip_hci import __version__ # TODO: replace this with importlib.metadata.version
-
         try:
             data = np.load(filename, allow_pickle=True)
         except BaseException:
@@ -89,7 +86,7 @@ def load(cls, filename):
             )
 
         file_vip_version = data["_vip_version"].item()
-        if file_vip_version != __version__:
+        if file_vip_version != version('vip_hci'):
             print(
                 "The file was saved with VIP {}. There may be some"
                 "compatibility issues. Use with care."