bump version (#475)

* warn if annotations will down-cast to float32

* correctly handle falsey data values

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.3
 
 [bumpversion:file:setup.py]
 search = version="{current_version}"

README.md

@@ -4,7 +4,7 @@
 
 `cellxgene` is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the [Human Cell Atlas](https://humancellatlas.org). Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data, and to demonstrate general, scalable, and reusable patterns for scientific data visualization.
 
-<img src="https://github.com/chanzuckerberg/cellxgene/blob/master/docs/cellxgene-demo-1.gif" width="200" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/blob/master/docs/cellxgene-demo-2.gif" width="200" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/blob/master/docs/cellxgene-demo-3.gif" width="200" height="200" hspace="30">
+<img src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-demo-1.gif" width="200" height="200" hspace="30"><img src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-demo-2.gif" width="200" height="200" hspace="30"><img src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-demo-3.gif" width="200" height="200" hspace="30">
 
 ## getting started
 
@@ -29,7 +29,7 @@ cellxgene launch pbmc3k.h5ad --open
 ```
 You should see your web browser open with the following
 
-<img width="450" src="https://github.com/chanzuckerberg/cellxgene/blob/master/docs/cellxgene-opening-screenshot.png" pad="50px">
+<img width="450" src="https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/docs/cellxgene-opening-screenshot.png" pad="50px">
 
 **Note**: automatic opening of the browser with the `--open` flag only works on OS X, on other platforms you'll need to directly point to the provided link in your browser.
 

client/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.2.1",
+  "version": "0.2.3",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "0.2.1",
+  "version": "0.2.3",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",

client/src/components/brushableHistogram/index.js

@@ -34,7 +34,7 @@ class HistogramBrush extends React.Component {
       .scaleLinear()
       .range([this.height - this.marginBottom, 0]);
 
-    if (obsAnnotations[0][field]) {
+    if (obsAnnotations[0][field] !== undefined) {
       // recalculate expensive stuff
       const allValuesForContinuousFieldAsArray = _.map(obsAnnotations, field);
 

docs/release_process.md

@@ -20,35 +20,36 @@ Follow these steps to create a release.
 
 1.  Preparation:
     - Define the release version number, using [semantic versioning](https://semver.org/)
-    - Write the release title and release notes
+    - Write the release title and release notes and add to 
+    [release notes document](https://docs.google.com/document/d/1KnHwkYfhyWO5H8BDcMu7y3ogjvq5Yi4OwpmZ8DB6w0Y/edit)
 2.  Create a release branch, eg, `release-version`
 3.  In the release branch:
-    - run `bumpversion --config-file .bumpversion.cfg [major | minor | patch]`
+    - Run `bumpversion --config-file .bumpversion.cfg [major | minor | patch]`
-    - clean up existing environment using `bin/clean`
+    - Clean up existing environment using `bin/clean`
-    - build the JS asserts using `bin/build-client`
+    - Build the JS asserts using `bin/build-client`
 4.  Commit and push the new branch
 5.  Create a PR for the release.
     - [optional] As needed, conduct PR review.
 6.  Merge to master
-7.  Create Github release using the version number and release notes ([instructions](https://help.github.com/articles/creating-releases/)).
+7.  Create Github release using the version number and release notes 
+([instructions](https://help.github.com/articles/creating-releases/)).
     - Draft new release
     - Type version name matching release version number from (1)
     - Select `master` as release branch (ensure you merged the release PR)
     - Type title `Release {version num}`
-    - [optional] check pre-release if this release is not ready for production
+    - [optional] Check pre-release if this release is not ready for production
     - Publish Release
- 8.  Publish to pypi by performing the following steps
+8.  Publish to pypi by performing the following steps (assumes you have `setuptools` and `twine` installed and that you 
-    (assumes you have `setuptools` and `twine` installed and that you have
+have registered for pypi and have write access to the cellxgene pypi package)
-    registered for pypi and have write access to the cellxgene pypi package)
+    - Build the distribution by calling
-    - build the distribution by calling
+    `python setup.py sdist`
-      `python setup.py sdist`
       inside the top-level directory
-    - [optional] upload the package to test pypi
+    - [optional] Upload the package to test pypi
       `twine upload --repository-url https://test.pypi.org/legacy/ dist/*`
-    - [optional] test the test installation in a fresh virtual environment using
+    - [optional] Test the test installation in a fresh virtual environment using
       `pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple cellxgene`
-    - upload the package to real pypi using `twine upload dist/*`
+    - Upload the package to real pypi using `twine upload dist/*`
-    - [optional] test the installation in a fresh virtual environment using
+    - [optional] Test the installation in a fresh virtual environment using
       `pip install cellxgene`
 
 The optional steps are for testing purposes, and are recommended

server/app/scanpy_engine/scanpy_engine.py

@@ -67,7 +67,9 @@ class ScanpyEngine(CXGDriver):
 
     @staticmethod
     def _can_cast_to_float32(ann):
-        if ann.dtype.kind == "f" and np.can_cast(ann.dtype, np.float32):
+        if ann.dtype.kind == "f":
+            if not np.can_cast(ann.dtype, np.float32):
+                warnings.warn(f"Annotation {ann.name} will be converted to 32 bit float and may loose precision.")
             return True
         return False
 

server/cli/cli.py

@@ -5,7 +5,7 @@ from .prepare import prepare
 
 
 @click.group(name="cellxgene", context_settings=dict(max_content_width=85))
-@click.version_option(version="0.2.1", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
+@click.version_option(version="0.2.3", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
 def cli():
     pass
 

setup.py

@@ -8,7 +8,7 @@ with open("server/requirements.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="0.2.1",
+    version="0.2.3",
     packages=find_packages(),
     url="https://github.com/chanzuckerberg/cellxgene",
     license="MIT",