Merge branch 'master' into imjoy

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 20.2.0-alpha.4
+current_version = 20.2.0-alpha.5
 parse = (?P<year>\d+)\.(?P<month>\d+)\.(?P<number>\d+)(\-(?P<release>[a-z]+)(\.(?P<build>\d+))?)?
 serialize = 
 	{year}.{month}.{number}-{release}.{build}

.circleci/config.yml

@@ -111,8 +111,10 @@ jobs:
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate tiktorch-server-env
-            ./scripts/conda_build.sh conda-recipe
             ./scripts/conda_build.sh conda-recipe-client
+            ./scripts/conda_build.sh pybio-core-recipe
+            ./scripts/conda_build.sh pybio-torch-recipe
+            ./scripts/conda_build.sh conda-recipe
 
 
 workflows:

conda-recipe/meta.yaml

@@ -16,7 +16,8 @@ build:
   number: {{ GIT_DESCRIBE_NUMBER }}
   script: python -m pip install --no-deps --ignore-installed .
   string: np{{CONDA_NPY}}py{{CONDA_PY}}_{{PKG_BUILDNUM}}_h{{PKG_HASH}}_g{{GIT_FULL_HASH[:7]}}
-
+  entrypoints:
+    - tiktorch-server = tiktorch.server.base:main
 
 requirements:
   build:
@@ -26,12 +27,13 @@ requirements:
     - h5py
     - python >=3.7
     - numpy >=1.14
+    - python-bioimage-io
+    - pytorch-bioimage-io
     - pyyaml
     - paramiko
-    - pytorch {{ pytorch_version }}*
-    - inferno {{ inferno_version }}*
-
+    - inferno
 
 test:
   imports:
-    - tiktorch
+    - tiktorch.server.base
+    - tiktorch.server.training

pybio-core-recipe/meta.yaml

@@ -0,0 +1,44 @@
+package:
+  name: python-bioimage-io
+  version: 0.1
+
+source:
+  git_url: https://github.com/bioimage-io/python-bioimage-io
+  git_rev: 67e2a060122d208c7ddd3f2908187b6b96716149
+
+build:
+  noarch: python
+  number: 0
+  script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed ."
+
+requirements:
+  host:
+    - python
+    - pip
+    - setuptools_scm
+  run:
+    - python
+    - scikit-learn
+    - requests
+    - marshmallow >=3.4,<3.5
+    - git
+    - pyyaml
+    - dataclasses >=0.6  # [py<37]
+
+test:
+  imports:
+    - pybio.spec
+
+about:
+  home: https://github.com/bioimage-io/python-bioimage-io
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: 'Tools for parsing pybio model specification'
+
+  doc_url: https://github.com/bioimage-io/python-bioimage-io
+  dev_url: https://github.com/bioimage-io/python-bioimage-io
+
+extra:
+  recipe-maintainers:
+    - m-novikov

pybio-torch-recipe/meta.yaml

@@ -0,0 +1,44 @@
+package:
+  name: pytorch-bioimage-io
+  version: 0.1
+
+source:
+  git_url: https://github.com/bioimage-io/pytorch-bioimage-io
+  git_rev: 02576f29e9c144d5bae68735fd10c9b7cf248859
+
+build:
+  number: 0
+  script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed ."
+
+requirements:
+  host:
+    - python
+    - pip
+    - setuptools_scm
+  run:
+    - python
+    - pytorch >=1.3,<1.5
+    - scikit-learn
+    - marshmallow >=3.4,<3.5
+    - python-bioimage-io
+    - pyyaml
+    - dataclasses >=0.6  # [py<37]
+
+test:
+  imports:
+    - pybio.torch
+    - pybio.torch.training
+
+about:
+  home: https://github.com/bioimage-io/pytorch-bioimage-io
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: 'Pytorch related components of pybio'
+
+  doc_url: https://github.com/bioimage-io/pytorch-bioimage-io
+  dev_url: https://github.com/bioimage-io/pytorch-bioimage-io
+
+extra:
+  recipe-maintainers:
+    - m-novikov

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name="tiktorch",
-    version="20.2.0-alpha.4",
+    version="20.2.0-alpha.5",
     description="Tiktorch client/server",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -25,7 +25,15 @@
         "Programming Language :: Python :: 3.7",
     ],
     packages=find_packages(exclude=["tests"]),  # Required
-    install_requires=["inferno-pytorch", "paramiko", "numpy", "pyyaml", "torch"],
+    install_requires=[
+        "inferno-pytorch",
+        "paramiko",
+        "numpy",
+        "pyyaml",
+        "torch",
+        "pybio.core @ git+ssh://[email protected]/m-novikov/python-bioimage-io#egg=pybio.core",
+        "pybio.torch @ git+ssh://[email protected]/m-novikov/pytorch-bioimage-io#egg=pybio.torch",
+    ],
     entry_points={"console_scripts": ["tiktorch=tiktorch.server.base:main"]},
     # extras_require={"test": ["pytest"]},
     project_urls={  # Optional