Restructured the code so that we can install the optional requiments …

…using `pip install -e ".[option]"`. To add optional requirements add to the [optional.extras_require] in the setup config. All functions and imports work the same way. Restructured the testing suite so it follows a similar pattern. All tests pass.

pyscicat/__init__.py

@@ -2,3 +2,5 @@
 
 __version__ = get_versions()["version"]
 del get_versions
+from . import hdf5
+from . import ingest

setup.cfg

@@ -4,3 +4,54 @@ style = pep440-post
 versionfile_source = pyscicat/_version.py
 versionfile_build = pyscicat/_version.py
 tag_prefix = v
+
+[metadata]
+
+name = pyscicat
+version = 1.0.0
+description = a python API to communicate with the Scicat API
+long_description = file: README.md
+long_description_content_type = text/markdown
+author = Dylan McReynolds
+author_email = "[email protected]",
+url = "https://github.com/scicatproject/pyscicat"
+license_file = LICENSE
+license="BSD (3-clause)"
+classifiers=
+        "Development Status :: 2 - Pre-Alpha"
+        "Natural Language :: English"
+        "Programming Language :: Python :: 3"
+
+
+[options]
+include_package_data = True
+install_requires =
+    pydantic
+    requests
+packages = find:
+python_requires  = >=3.8
+
+
+[options.extras_require]
+hdf5 =
+        hdf5plugin
+        h5py
+dev =
+    codecov
+    coverage
+    flake8
+    pytest
+    sphinx
+    twine
+    black
+    requests_mock
+docs =
+    ipython
+    matplotlib
+    mistune <2.0.0  # temporary while sphinx sorts this out
+    myst-parser
+    numpydoc
+    sphinx-click
+    sphinx-copybutton
+    sphinxcontrib.openapi
+    sphinx_rtd_theme

setup.py

@@ -1,68 +1,6 @@
 from pathlib import Path
 from setuptools import setup, find_packages
 import sys
-import versioneer
 
-min_version = (3, 7)
-if sys.version_info < min_version:
-    error = """
-pyscicat does not support Python {0}.{1}.
-Python {2}.{3} and above is required. Check your Python version like so:
+setup()
 
-python3 --version
-
-This may be due to an out-of-date pip. Make sure you have pip >= 9.0.1.
-Upgrade pip like so:
-
-pip install --upgrade pip
-""".format(
-        *(sys.version_info[:2] + min_version)
-    )
-    sys.exit(error)
-
-here = Path(__file__).absolute()
-
-with open(here.with_name("README.md"), encoding="utf-8") as readme_file:
-    readme = readme_file.read()
-
-
-def read_requirements_from_here(here: Path, filename: str = None) -> list:
-    assert filename is not None, "filename as string must be provided"
-    assert here.with_name(
-        filename
-    ).exists(), f"requirements filename {filename} does not exist"
-    with open(here.with_name(filename)) as requirements_file:
-        # Parse requirements.txt, ignoring any commented-out lines.
-        requirements = [
-            line
-            for line in requirements_file.read().splitlines()
-            if not line.startswith("#")
-        ]
-    return requirements
-
-
-extras_require = {}
-extras_require["base"] = read_requirements_from_here(here, "requirements.txt")
-extras_require["h5tools"] = read_requirements_from_here(here, "requirements-hdf5.txt")
-
-setup(
-    name="pyscicat",
-    version=versioneer.get_version(),
-    cmdclass=versioneer.get_cmdclass(),
-    description="Code for communicating to a SciCat backend server python",
-    long_description=readme,
-    author="Dylan McReynolds",
-    author_email="[email protected]",
-    url="https://github.com/scicatproject/pyscicat",
-    python_requires=">={}".format(".".join(str(n) for n in min_version)),
-    packages=find_packages(exclude=["docs", "tests"]),
-    include_package_data=True,
-    extras_require=extras_require,
-    install_requires=extras_require["base"],
-    license="BSD (3-clause)",
-    classifiers=[
-        "Development Status :: 2 - Pre-Alpha",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3",
-    ],
-)

pyscicat/hdf5/_tests/test_hdf5sct.py → tests/test_hdf5/test_hdf5sct.py

@@ -9,19 +9,19 @@
 
 def test_readValue():
     # more intelligent path finding:
-    p = sorted(Path(".").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
+    p = sorted(Path("").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
     v = h5Get(p, "/sasentry1/sasdata1/I")
     assert v != "none", "Did not extract value"
 
 
 def test_readAttribute():
-    p = sorted(Path(".").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
+    p = sorted(Path("").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
     v = h5Get(p, "/sasentry1/sasdata1@timestamp")
     assert v != "none", "Did not extract attribute"
 
 
 def test_readMixedDict():
-    p = sorted(Path(".").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
+    p = sorted(Path("").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
     v = h5GetDict(
         p,
         {
@@ -38,7 +38,7 @@ def test_readMixedDict():
 
 
 def test_readMetadata_withroot():
-    p = sorted(Path(".").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
+    p = sorted(Path("").glob("**/cylinderHex_r5_s12_T50_large_ranW_0p5.nxs"))[0]
     assert p.exists(), f"HDF5/NeXus test file: {p.as_posix()} cannot be found"
     resultDict = scientific_metadata(p, excludeRootEntry=True, skipKeyList=["sasdata1"])
     assert resultDict is not None, "scientific_metadata has not returned anything"

pyscicat/tests/test_client.py → tests/test_pyscicat/test_client.py

@@ -3,7 +3,7 @@
 
 import pytest
 import requests_mock
-from ..client import (
+from pyscicat.client import (
     from_credentials,
     from_token,
     encode_thumbnail,
@@ -12,7 +12,7 @@
     ScicatCommError,
 )
 
-from ..model import (
+from pyscicat.model import (
     Attachment,
     Datablock,
     DataFile,