Merge pull request #21 from cryoem-uoft/release-v4.2

Release v4.2.0

.gitignore

@@ -64,5 +64,7 @@ ipython_config.py
 
 # Other
 .ruff_cache
+.vercel
 cryosparc/core.c
 *.dSYM
+Python-*

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## v4.2.0
+
+- Support for CryoSPARC v4.2
+
 ## v4.1.3
 
 - Fix error when creating a job with `CryoSPARC.create_job`

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2022 Structura Biotechnology Inc.
+Copyright 2023 Structura Biotechnology Inc.
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

Makefile

@@ -1,17 +1,68 @@
 # Actual target is a .so file with a dynamically-determined name, but this is
 # close enough
 TARGET=cryosparc/core.c
+PYTHON=python3.9
+PYTHON_VERSION=3.9.16
 
 all: $(TARGET)
 
+# -----------------------------------------------------------------------------
+#    Primary build target
+# -----------------------------------------------------------------------------
+
 $(TARGET): cryosparc/include/cryosparc-tools/*.h cryosparc/dataset.c cryosparc/*.pyx cryosparc/*.pxd setup.py pyproject.toml
 	python -m setup build_ext -i
 
+# -----------------------------------------------------------------------------
+#    Vercel deployment-related targets
+# -----------------------------------------------------------------------------
+
+Python-$(PYTHON_VERSION).tgz:
+	curl -L https://www.python.org/ftp/python/$(PYTHON_VERSION)/Python-$(PYTHON_VERSION).tgz -o Python-$(PYTHON_VERSION).tgz
+
+Python-$(PYTHON_VERSION): Python-$(PYTHON_VERSION).tgz
+	tar -xzf Python-${PYTHON_VERSION}.tgz
+
+python: Python-$(PYTHON_VERSION)
+	cd Python-$(PYTHON_VERSION) && ./configure && cd .. || cd ..
+	make -C Python-$(PYTHON_VERSION)
+	make -C Python-$(PYTHON_VERSION) altinstall
+
+.venv/bin/python:
+	$(PYTHON) -m venv .venv
+
+.venv/bin/pip: .venv/bin/python
+	.venv/bin/python -m pip install -U pip
+
+.venv/bin/jupyter-book: .venv/bin/pip
+	.venv/bin/pip install -e ".[build]"
+
+.vercel/output/config.json:
+	mkdir -p .vercel/output
+	echo '{"version":3,"cache":[".venv/**","build/**","docs/_build/**","Python-*.tgz","Python-*/**"]}' > .vercel/output/config.json
+
+verceldeps:
+	yum update -y
+	yum install bzip2-devel libffi-devel openssl-devel sqlite-devel -y
+
+vercelinstall: verceldeps python .venv/bin/python
+	echo "Install complete"
+
+vercelbuild: .vercel/output/config.json .venv/bin/jupyter-book
+	.venv/bin/jupyter-book build docs
+	rm -rf .vercel/output/static && cp -R docs/_build/html .vercel/output/static
+
+# -----------------------------------------------------------------------------
+#    Cleanup
+# -----------------------------------------------------------------------------
+
 clean:
+	rm -f $(TARGET)
+	rm -f *.tgz *.tar.gz
 	rm -f cryosparc/*.so
-	rm -f cryosparc/core.c
 	rm -rf build
 	rm -rf dist
 	rm -rf *.egg-info
+	rm -rf Python-$(PYTHON_VERSION)
 
-.PHONY: clean all
+.PHONY: clean all python verceldeps vercelinstall vercelbuild

cryosparc/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "4.1.3"
+__version__ = "4.2.0"
 
 
 def get_include():

cryosparc/job.py

@@ -40,6 +40,12 @@ class Job(MongoController[JobDocument]):
     outputs, add to job log, download job files. Should be instantiated
     through `CryoSPARC.find_job`_ or `Project.find_job`_.
 
+    Attributes:
+        uid (str): Job unique ID, e.g., "J42"
+        project_uid (str): Project unique ID, e.g., "P3"
+        doc (JobDocument): All job data from the CryoSPARC database. Database
+            contents may change over time, use the `refresh`_ method to update.
+
     Examples:
 
         Find an existing job.
@@ -70,6 +76,9 @@ class Job(MongoController[JobDocument]):
 
     .. _Project.find_job:
         project.html#cryosparc.project.Project.find_job
+
+    .. _refresh:
+        #cryosparc.job.Job.refresh
     """
 
     def __init__(self, cs: "CryoSPARC", project_uid: str, uid: str) -> None:
@@ -926,7 +935,14 @@ class ExternalJob(Job):
     an input. Its outputs must be created manually and may be configured to
     passthrough inherited input fields, just as with regular CryoSPARC jobs.
 
-    Create a new External Job with `Project.create_external_job`_.
+    Create a new External Job with `Project.create_external_job`_. ExternalJob
+    is a subclass of `Job`_ and inherits all its methods.
+
+    Attributes:
+        uid (str): Job unique ID, e.g., "J42"
+        project_uid (str): Project unique ID, e.g., "P3"
+        doc (JobDocument): All job data from the CryoSPARC database. Database
+            contents may change over time, use the `refresh`_ method to update.
 
     Examples:
 
@@ -946,9 +962,14 @@ class ExternalJob(Job):
         ...     dset['movie_blob/path'] = ...  # populate dataset
         ...     job.save_output(output_name, dset)
 
+    .. _Job:
+        #cryosparc.job.Job
+
+    .. _refresh:
+        #cryosparc.job.Job.refresh
+
     .. _Project.create_external_job:
         project.html#cryosparc.project.Project.create_external_job
-
     """
 
     def add_input(

cryosparc/project.py

@@ -19,8 +19,17 @@ class Project(MongoController[ProjectDocument]):
     and upload/download project files. Should be instantiated through
     `CryoSPARC.find_project`_.
 
+    Attributes:
+        uid (str): Project unique ID, e.g., "P3"
+        doc (ProjectDocument): All project data from the CryoSPARC database.
+            Database contents may change over time, use the `refresh`_ method
+            to update.
+
     .. _CryoSPARC.find_project:
         tools.html#cryosparc.tools.CryoSPARC.find_project
+
+    .. _refresh:
+        #cryosparc.project.Project.refresh
     """
 
     def __init__(self, cs: "CryoSPARC", uid: str) -> None:

cryosparc/workspace.py

@@ -15,11 +15,21 @@ class Workspace(MongoController[WorkspaceDocument]):
     results. Should be instantiated through `CryoSPARC.find_workspace`_ or
     `Project.find_workspace`_.
 
+    Attributes:
+        uid (str): Workspace unique ID, e.g., "W42"
+        project_uid (str): Project unique ID, e.g., "P3"
+        doc (WorkspaceDocument): All workspace data from the CryoSPARC database.
+            Database contents may change over time, use the `refresh`_ method
+            to update.
+
     .. _CryoSPARC.find_workspace:
         tools.html#cryosparc.tools.CryoSPARC.find_workspace
 
     .. _Project.find_workspace:
         project.html#cryosparc.project.Project.find_workspace
+
+    .. _refresh:
+        #cryosparc.workspace.Workspace.refresh
     """
 
     def __init__(self, cs: "CryoSPARC", project_uid: str, uid: str) -> None:

docs/_config.yml

@@ -33,7 +33,7 @@ html:
   use_repository_button: true
   extra_footer: |
     <p>
-      © 2022 Structura Biotechnology Inc. Toronto, Canada<br>
+      © 2023 Structura Biotechnology Inc. Toronto, Canada<br>
       CryoSPARC and CryoSPARC Live are trademarks of Structura Biotechnology Inc.
     </p>
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cryosparc-tools"
-version = "4.1.3"
+version = "4.2.0"
 description = "Toolkit for interfacing with CryoSPARC"
 readme = "README.md"
 requires-python = ">=3.7"
@@ -40,7 +40,6 @@ dev = [
 
 build = [
     "build",
-    "black[jupyter]",
     "autodocsumm",
     "cython",
     "jupyter-book",

setup.py

@@ -23,7 +23,7 @@
 
 setup(
     name="cryosparc_tools",
-    version="4.1.3",
+    version="4.2.0",
     description="Toolkit for interfacing with CryoSPARC",
     headers=["cryosparc/include/cryosparc-tools/dataset.h"],
     ext_modules=cythonize(

vercel.json

@@ -0,0 +1,6 @@
+{
+    "framework": null,
+    "installCommand": "make vercelinstall",
+    "buildCommand": "make vercelbuild",
+    "outputDirectory": "docs/_build/html"
+}