Merge pull request #177 from AllenInstitute/develop

Develop

Author: RussTorres

.gitignore

@@ -15,4 +15,5 @@ htmlcov/
 .pytest_cache
 .vscode
 .idea/
-*.iml
+*.iml
+.pixi/

integration_tests/test_stack_integrated.py

@@ -32,7 +32,8 @@ def render():
 
 @pytest.fixture
 def simpletilespec():
-    mml = renderapi.image_pyramid.MipMapLevel(0, '/not/a/path.jpg')
+    mm = renderapi.image_pyramid.MipMap(imageUrl='file://not/a/path.jpg')
+    ip = renderapi.image_pyramid.ImagePyramid({0: mm})
     tform = renderapi.transform.AffineModel(labels=['simple'])
     layout = renderapi.tilespec.Layout(sectionId="section0",
                                        scopeId="testscope",
@@ -45,7 +46,7 @@ def simpletilespec():
     ts = renderapi.tilespec.TileSpec(tileId="1000",
                                      width=2048,
                                      height=2048,
-                                     mipMapLevels=[mml],
+                                     imagePyramid=ip,
                                      z=0,
                                      tforms=[tform],
                                      layout=layout)

pyproject.toml

@@ -0,0 +1,94 @@
+[project]
+name = "render-python"
+description = "python API client to interact with render databases (see https://github.com/saalfeldlab/render)"
+readme = "README.rst"
+license = {file = "LICENSE"}
+authors = [
+  {name = "Forrest Collman"},
+  {name = "Russel Torres"},
+  {name = "Eric Perlman"},
+  {name = "Sharmi Seshamani"}
+]
+maintainers = [
+  {name = "Russel Torres"}
+]
+requires-python = ">3.8,<3.12"
+dynamic = ["version"]
+dependencies = [
+    "requests",
+    "scipy",
+    "numpy",
+    "pillow",
+    "sphinxcontrib-napoleon",
+    "decorator",
+    "six"
+]
+
+[project.urls]
+Repository = "https://github.com/AllenInstitute/render-python.git"
+
+[project.optional-dependencies]
+test = [
+    "coverage>=4.1",
+    "mock>=2.0.0",
+    "pep8>=1.7.0",
+    # "pytest>4.6,<5.0",
+    "pytest",
+    "pytest-cov>=2.2.1",
+    "pytest-pep8>=1.0.6",
+    "pytest-xdist>=1.14",
+    "flake8>=3.0.4",
+    "pylint>=1.5.4",
+    "jinja2",
+    "ujson"
+]
+pypi-build = [
+    "build",
+    "twine"
+]
+
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+py-modules = [
+    "renderapi"
+]
+
+[tool.setuptools_scm]
+version_file = "renderapi/_version.py"
+
+# some downgrades from pixi's expectations
+[tool.pixi.system-requirements]
+linux = "5.0.0"
+libc = "2.27"
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[tool.pixi.pypi-dependencies]
+render-python = { path = ".", editable = true }
+
+# conda-enabled features
+[tool.pixi.feature.pixi-base.dependencies]
+numpy = "*"
+scipy = "*"
+
+[tool.pixi.environments]
+test = ["test"]
+conda = ["pixi-base"]
+conda-test = ["pixi-base", "test"]
+build = ["pypi-build"]
+
+[tool.coverage.run]
+omit = ["integration_tests/*", "test/*"]
+
+[tool.pixi.feature.test.tasks]
+test = "pytest  --cov --cov-report=xml --junitxml=test-reports/test.xml"
+
+[tool.pixi.feature.pypi-build.tasks]
+pypi-build = "python -m build"
+pypi-test-upload = "python -m twine upload --repository testpypi dist/*"
+pypi-test-deploy = "python -m build && python -m twine upload --repository testpypi dist/*"

renderapi/coordinate.py

@@ -6,7 +6,6 @@
 from .utils import NullHandler, renderdumps, renderdump, get_json
 from .client import coordinateClient
 from .errors import RenderError
-import requests
 import json
 import numpy as np
 import logging
@@ -20,7 +19,7 @@
 @renderaccess
 def world_to_local_coordinates(stack, z, x, y, host=None,
                                port=None, owner=None, project=None,
-                               session=requests.session(),
+                               session=None,
                                render=None, **kwargs):
     """maps an world x,y,z coordinate in stack to a local coordinate
     Parameters
@@ -64,7 +63,7 @@ def world_to_local_coordinates(stack, z, x, y, host=None,
 @renderaccess
 def local_to_world_coordinates(stack, tileId, x, y,
                                host=None, port=None, owner=None, project=None,
-                               session=requests.session(),
+                               session=None,
                                render=None, **kwargs):
     """convert coordinate from local to world with webservice request
 
@@ -110,7 +109,7 @@ def local_to_world_coordinates(stack, tileId, x, y,
 def world_to_local_coordinates_batch(stack, d, z, host=None,
                                      port=None, owner=None, project=None,
                                      execute_local=False,
-                                     session=requests.session(),
+                                     session=None,
                                      render=None, **kwargs):
 
     """convert coordinate parameters from world to local
@@ -174,7 +173,7 @@ def world_to_local_coordinates_batch(stack, d, z, host=None,
 @renderaccess
 def local_to_world_coordinates_batch(stack, d, z, host=None,
                                      port=None, owner=None, project=None,
-                                     session=requests.session(),
+                                     session=None,
                                      render=None, **kwargs):
     """convert coordinate parameters from local to world
 
@@ -302,7 +301,7 @@ def unpackage_world_to_local_point_match_from_json(json_answer, tileId):
 # def old_world_to_local_coordinates_array(stack, dataarray, tileId, z=0,
 #                                          host=None, port=None,
 #                                          owner=None, project=None,
-#                                          session=requests.session(),
+#                                          session=None,
 #                                          render=None, **kwargs):
 #     ''''''
 
@@ -359,7 +358,7 @@ def world_to_local_coordinates_array(stack, dataarray, tileId, z,
                                      owner=None, project=None,
                                      client_script=None,
                                      doClientSide=False, number_of_threads=20,
-                                     session=requests.session(), **kwargs):
+                                     session=None, **kwargs):
     """map world to local coordinates using numpy array
 
     Parameters
@@ -403,7 +402,7 @@ def world_to_local_coordinates_array(stack, dataarray, tileId, z,
 # def old_local_to_world_coordinates_array(stack, dataarray, tileId, z=0,
 #                                          host=None, port=None,
 #                                          owner=None, project=None,
-#                                          session=requests.session(),
+#                                          session=None,
 #                                          render=None, **kwargs):
 #     ''''''
 #     request_url = format_preamble(
@@ -439,7 +438,7 @@ def local_to_world_coordinates_array(stack, dataarray, tileId, z,
                                      owner=None, project=None,
                                      client_script=None,
                                      doClientSide=False, number_of_threads=20,
-                                     session=requests.session(), **kwargs):
+                                     session=None, **kwargs):
     """map local to world coordinates using numpy array
 
     Parameters

renderapi/image.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import io
-import requests
 from PIL import Image
 import numpy as np
 import logging
@@ -36,7 +35,7 @@ def get_bb_renderparams(stack, z, x, y, width, height, scale=1.0,
                         binaryMask=None, filter=None, filterListName=None,
                         convertToGray=None, excludeMask=None,
                         host=None, port=None, owner=None,
-                        project=None, session=requests.session(),
+                        project=None, session=None,
                         render=None, **kwargs):
 
     request_url = format_preamble(
@@ -63,7 +62,7 @@ def get_bb_image(stack, z, x, y, width, height, scale=1.0,
                  minIntensity=None, maxIntensity=None, binaryMask=None,
                  filter=None, maxTileSpecsToRender=None,
                  host=None, port=None, owner=None, project=None,
-                 img_format=None, session=requests.session(),
+                 img_format=None, session=None,
                  render=None, **kwargs):
     """render image from a bounding box defined in xy and return numpy array:
 
@@ -150,7 +149,7 @@ def get_tile_renderparams(
         filter=None, filterListName=None, excludeMask=None, convertToGray=None,
         binaryMask=None, host=None, port=None, owner=None,
         project=None, img_format=None,
-        session=requests.session(), render=None, **kwargs):
+        session=None, render=None, **kwargs):
     request_url = format_preamble(
         host, port, owner, project, stack) + \
         "/tile/%s/render-parameters" % (
@@ -182,7 +181,7 @@ def get_tile_image_data(stack, tileId, channel=None, normalizeForMatching=True,
                         minIntensity=None, maxIntensity=None,
                         filter=None, host=None, port=None, owner=None,
                         project=None, img_format=None,
-                        session=requests.session(), render=None, **kwargs):
+                        session=None, render=None, **kwargs):
     """render image from a tile with all transforms and return numpy array
 
     :func:`renderapi.render.renderaccess` decorated function
@@ -273,7 +272,7 @@ def get_section_renderparams(stack, z, binaryMask=None, channel=None,
                              filterListName=None, minIntensity=None,
                              maxIntensity=None, scale=None,
                              host=None, port=None, owner=None, project=None,
-                             session=requests.session(),
+                             session=None,
                              render=None, **kwargs):
     request_url = format_preamble(
         host, port, owner, project, stack) + "/z/{}/render-parameters".format(
@@ -299,7 +298,7 @@ def get_section_image(stack, z, scale=1.0, channel=None,
                       filter=False,
                       maxTileSpecsToRender=None, img_format=None,
                       host=None, port=None, owner=None, project=None,
-                      session=requests.session(),
+                      session=None,
                       render=None, **kwargs):
     """render an section of image
 
@@ -371,7 +370,7 @@ def get_section_image(stack, z, scale=1.0, channel=None,
 @renderaccess
 def get_renderparameters_image(renderparams, img_format=None,
                                host=None, port=None, owner=None,
-                               session=requests.session(),
+                               session=None,
                                render=None, **kwargs):
     try:
         image_ext = IMAGE_FORMATS[img_format]