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Code Issues Packages Projects Releases Wiki Activity

Makefile modularity, test targets, and auto-formatting (#1070)

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* Fix Makefile whitespace and .PHONY use

* Fix Makefile filename

* Modularize Makefile into client and server Makefiles

Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.

This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.

* Add auto-formatting to client and server modules

One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.

* Add yapf for automatic code formatting

* Add a root test target that calls sub-tests

* Apply yapf to python files

* Do not duplicate npm commands, simply pass through

* Update documentation

* Do not shadow reserved word len

* Add general test target

* Fix make call in dev-env

* Use black instead of yapf

* Run flake8 from the root directory

* Revert "Apply yapf to python files"

This reverts commit cdca128a01.

* Apply black to python code

* Resolve lint errors resulting from black format

* Add explanation of server unit tests in dev guidelines
This commit is contained in:
Matt Weiden
2019-12-27 14:43:37 -08:00
committed by GitHub
parent ec79995be8
commit f3015cb9df
37 changed files with 738 additions and 806 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/gui/browser.py
+3 -4
View File
@@ -12,6 +12,7 @@ WindowUtils = cef.WindowUtils()
# noinspection PyUnresolvedReferences
CefWidgetParent = QWidget
class CefWidget(CefWidgetParent):
def __init__(self, parent=None):
super(CefWidget, self).__init__(parent)
@@ -58,8 +59,7 @@ class CefWidget(CefWidgetParent):
if WINDOWS:
WindowUtils.OnSize(self.getHandle(), 0, 0, 0)
elif LINUX:
self.browser.SetBounds(self.x, self.y,
self.width(), self.height())
self.browser.SetBounds(self.x, self.y, self.width(), self.height())
self.browser.NotifyMoveOrResizeStarted()
def resizeEvent(self, event):
@@ -68,8 +68,7 @@ class CefWidget(CefWidgetParent):
if WINDOWS:
WindowUtils.OnSize(self.getHandle(), 0, 0, 0)
elif LINUX:
self.browser.SetBounds(self.x, self.y,
size.width(), size.height())
self.browser.SetBounds(self.x, self.y, size.width(), size.height())
self.browser.NotifyMoveOrResizeStarted()
server/gui/hook-cefpython3.py
+22 -26
View File
@@ -37,8 +37,7 @@ logger = logging.getLogger(__name__)
# Functions
def check_platforms():
if not is_win and not is_darwin and not is_linux:
raise SystemExit("Error: Currently only Windows, Linux and Darwin "
"platforms are supported, see Issue #135.")
raise SystemExit("Error: Currently only Windows, Linux and Darwin " "platforms are supported, see Issue #135.")
def check_pyinstaller_version():
@@ -50,22 +49,19 @@ def check_pyinstaller_version():
version = PyInstaller.__version__
match = re.search(r"^\d+\.\d+(\.\d+)?", version)
if not (match.group(0) >= PYINSTALLER_MIN_VERSION):
raise SystemExit("Error: pyinstaller %s or higher is required"
% PYINSTALLER_MIN_VERSION)
raise SystemExit("Error: pyinstaller %s or higher is required" % PYINSTALLER_MIN_VERSION)
def check_cefpython3_version():
if not is_module_satisfies("cefpython3 >= %s" % CEFPYTHON_MIN_VERSION):
raise SystemExit("Error: cefpython3 %s or higher is required"
% CEFPYTHON_MIN_VERSION)
raise SystemExit("Error: cefpython3 %s or higher is required" % CEFPYTHON_MIN_VERSION)
def get_cefpython_modules():
"""Get all cefpython Cython modules in the cefpython3 package.
It returns a list of names without file extension. Eg.
'cefpython_py27'. """
pyds = glob.glob(os.path.join(CEFPYTHON3_DIR,
"cefpython_py*" + CYTHON_MODULE_EXT))
pyds = glob.glob(os.path.join(CEFPYTHON3_DIR, "cefpython_py*" + CYTHON_MODULE_EXT))
assert len(pyds) > 1, "Missing cefpython3 Cython modules"
modules = []
for path in pyds:
@@ -130,14 +126,21 @@ def get_cefpython3_datas():
for filename in os.listdir(CEFPYTHON3_DIR):
# Ignore Cython modules which are already handled by
# pyinstaller automatically.
if filename[:-len(CYTHON_MODULE_EXT)] in get_cefpython_modules():
if filename[: -len(CYTHON_MODULE_EXT)] in get_cefpython_modules():
continue
# CEF binaries and datas
extension = os.path.splitext(filename)[1]
if extension in \
[".exe", ".dll", ".pak", ".dat", ".bin", ".txt", ".so", ".plist"] \
or filename.lower().startswith("license"):
if extension in [
".exe",
".dll",
".pak",
".dat",
".bin",
".txt",
".so",
".plist",
] or filename.lower().startswith("license"):
logger.info("Include cefpython3 data: {}".format(filename))
ret.append((os.path.join(CEFPYTHON3_DIR, filename), cefdatadir))
@@ -145,11 +148,9 @@ def get_cefpython3_datas():
# "Chromium Embedded Framework.framework/Resources" with subdirectories
# is required. Contain .pak files and locales (each locale in separate
# subdirectory).
resources_subdir = \
os.path.join("Chromium Embedded Framework.framework", "Resources")
resources_subdir = os.path.join("Chromium Embedded Framework.framework", "Resources")
base_path = os.path.join(CEFPYTHON3_DIR, resources_subdir)
assert os.path.exists(base_path), \
"{} dir not found in cefpython3".format(resources_subdir)
assert os.path.exists(base_path), "{} dir not found in cefpython3".format(resources_subdir)
for path, dirs, files in os.walk(base_path):
for file in files:
absolute_file_path = os.path.join(path, file)
@@ -159,22 +160,17 @@ def get_cefpython3_datas():
elif is_win or is_linux:
# The .pak files in cefpython3/locales/ directory
locales_dir = os.path.join(CEFPYTHON3_DIR, "locales")
assert os.path.exists(locales_dir), \
"locales/ dir not found in cefpython3"
assert os.path.exists(locales_dir), "locales/ dir not found in cefpython3"
for filename in os.listdir(locales_dir):
logger.info("Include cefpython3 data: {}/{}".format(
os.path.basename(locales_dir), filename))
ret.append((os.path.join(locales_dir, filename),
os.path.join(cefdatadir, "locales")))
logger.info("Include cefpython3 data: {}/{}".format(os.path.basename(locales_dir), filename))
ret.append((os.path.join(locales_dir, filename), os.path.join(cefdatadir, "locales")))
# Optional .so/.dll files in cefpython3/swiftshader/ directory
swiftshader_dir = os.path.join(CEFPYTHON3_DIR, "swiftshader")
if os.path.isdir(swiftshader_dir):
for filename in os.listdir(swiftshader_dir):
logger.info("Include cefpython3 data: {}/{}".format(
os.path.basename(swiftshader_dir), filename))
ret.append((os.path.join(swiftshader_dir, filename),
os.path.join(cefdatadir, "swiftshader")))
logger.info("Include cefpython3 data: {}/{}".format(os.path.basename(swiftshader_dir), filename))
ret.append((os.path.join(swiftshader_dir, filename), os.path.join(cefdatadir, "swiftshader")))
return ret
server/gui/main.py
+17 -11
View File
@@ -20,8 +20,8 @@ from server.utils.utils import find_available_port
if WINDOWS or LINUX:
dirname = dirname(PySide2.__file__)
plugin_path = join(dirname, 'plugins', 'platforms')
environ['QT_QPA_PLATFORM_PLUGIN_PATH'] = plugin_path
plugin_path = join(dirname, "plugins", "platforms")
environ["QT_QPA_PLATFORM_PLUGIN_PATH"] = plugin_path
# Configuration
# TODO remember this or calculate it?
@@ -94,8 +94,7 @@ class MainWindow(QMainWindow):
# a hidden window, embed CEF browser in it and then
# create a container for that hidden window and replace
# cef widget in the layout with the container.
self.container = QWidget.createWindowContainer(
self.cef_widget.hidden_window, parent=self)
self.container = QWidget.createWindowContainer(self.cef_widget.hidden_window, parent=self)
self.stacked_layout.replaceWidget(self.cef_widget, self.container)
self.stacked_layout.setCurrentIndex(LOAD_INDEX)
@@ -117,7 +116,7 @@ class MainWindow(QMainWindow):
def setupMenu(self):
# TODO add communication to subprocess on reload
main_menu = self.menuBar()
file_menu = main_menu.addMenu('File')
file_menu = main_menu.addMenu("File")
load_action = QAction("Load file...", self)
load_action.setStatusTip("Load file")
load_action.setShortcut("Ctrl+O")
@@ -201,7 +200,7 @@ class LoadWidget(QFrame):
for l in [logo_layout, file_layout, message_layout]:
load_ui_layout.addLayout(l)
#TODO remove magic number
# TODO remove magic number
load_ui_layout.setStretch(1, 10)
self.setLayout(load_ui_layout)
@@ -240,8 +239,15 @@ class LoadWidget(QFrame):
def createScanpyEngine(self, file_name):
title = splitext(basename(file_name))[0]
self.window().setupServer()
worker = Worker(self.window().parent_conn, self.window().child_conn, file_name, host="127.0.0.1",
port=GUI_PORT, title=title, engine_options={})
worker = Worker(
self.window().parent_conn,
self.window().child_conn,
file_name,
host="127.0.0.1",
port=GUI_PORT,
title=title,
engine_options={},
)
self.window().load_emitter.signals.ready.connect(self.onDataReady)
self.window().load_emitter.signals.engine_error.connect(self.onServerError)
self.window().load_emitter.signals.server_error.connect(self.onServerError)
@@ -289,6 +295,7 @@ class LoadWidget(QFrame):
onServerError = partialmethod(onError, server_error=True)
class FilePath(QObject):
def __init__(self):
super(FilePath, self).__init__()
@@ -320,8 +327,7 @@ class FileArea(QFrame):
def fileBrowse(self):
options = QFileDialog.Options()
# options |= QFileDialog.DontUseNativeDialog
file_name, _ = QFileDialog.getOpenFileName(self,
"Open H5AD File", "", "H5AD Files (*.h5ad)", options=options)
file_name, _ = QFileDialog.getOpenFileName(self, "Open H5AD File", "", "H5AD Files (*.h5ad)", options=options)
if file_name:
self.parent().file_name.updateValue(file_name)
self.parent().onLoad()
@@ -391,5 +397,5 @@ def main():
sys.exit(0)
if __name__ == '__main__':
if __name__ == "__main__":
main()
server/gui/utils.py
+5 -3
View File
@@ -4,9 +4,9 @@ import platform
from PySide2.QtCore import QObject, Signal
# Detect OS
WINDOWS = (platform.system() == "Windows")
LINUX = (platform.system() == "Linux")
MAC = (platform.system() == "Darwin")
WINDOWS = platform.system() == "Windows"
LINUX = platform.system() == "Linux"
MAC = platform.system() == "Darwin"
class WorkerSignals(QObject):
@@ -18,6 +18,7 @@ class WorkerSignals(QObject):
error - `str` error message
result - `object` data returned from processing, anything
"""
finished = Signal()
engine_error = Signal(str)
server_error = Signal(str)
@@ -34,6 +35,7 @@ class SiteReadySignals(QObject):
ready
error - `str` error message
"""
ready = Signal()
timeout = Signal()
error = Signal(str)
server/gui/workers.py
+1
View File
@@ -36,6 +36,7 @@ class Worker(EmittingProcess):
return
from server.app.app import Server
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
# create server
try:
server = Server()