Installer (#840)

.bumpversion.cfg

@@ -13,3 +13,7 @@ replace = version="{new_version}"
 search = "version": "{current_version}"
 replace = "version": "{new_version}"
 
+[bumpversion:file:server/__init__.py]
+search = "__version__ = "{current_version}"
+replace = "__version__ = "{new_version}"
+

cellxgene-osx.spec

@@ -0,0 +1,41 @@
+# -*- mode: python ; coding: utf-8 -*-
+
+block_cipher = None
+
+
+a = Analysis(['server/gui/main.py'],
+             pathex=['/Users/charlotteweaver/Documents/Git/cellxgene'],
+             binaries=[('/System/Library/Frameworks/Tk.framework/Tk', 'tk'), ('/System/Library/Frameworks/Tcl.framework/Tcl', 'tcl')],
+             datas=[('server/app/web/templates/', 'server/app/web/templates/'), ('server/app/web/static/', 'server/app/web/static/')],
+             hiddenimports=['sklearn', 'sklearn.utils._cython_blas', 'sklearn.neighbors.typedefs', 'sklearn.neighbors.quad_tree', 'sklearn.tree', 'sklearn.tree._utils'],
+             hookspath=['server/gui/'],
+             runtime_hooks=[],
+             excludes=[],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher,
+             noarchive=False)
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+exe = EXE(pyz,
+          a.scripts,
+          [],
+          exclude_binaries=True,
+          name='cellxgene',
+          debug=False,
+          bootloader_ignore_signals=False,
+          strip=False,
+          upx=True,
+          console=False , icon='server/gui/images/cxg_icons.icns')
+coll = COLLECT(exe,
+               a.binaries,
+               a.zipfiles,
+               a.datas,
+               strip=False,
+               upx=True,
+               upx_exclude=[],
+               name='cellxgene')
+app = BUNDLE(coll,
+             name='cellxgene.app',
+             icon='server/gui/images/cxg_icons.icns',
+             bundle_identifier=None)

cellxgene-windows.spec

@@ -0,0 +1,36 @@
+# -*- mode: python -*-
+
+block_cipher = None
+
+
+a = Analysis(['server\\gui\\main.py'],
+             pathex=['C:\\Users\\Charlotte\\Documents\\git\\cellxgene'],
+             binaries=[],
+             datas=[('server/app/web/templates/', 'server/app/web/templates'), ('server/app/web/static/', 'server/app/web/static')],
+             hiddenimports=[],
+             hookspath=['server/gui/'],
+             runtime_hooks=[],
+             excludes=[],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher,
+             noarchive=False)
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+exe = EXE(pyz,
+          a.scripts,
+          [],
+          exclude_binaries=True,
+          name='cellxgene',
+          debug=False,
+          bootloader_ignore_signals=False,
+          strip=False,
+          upx=True,
+          console=False , icon='server\\gui\\images\\icon.ico')
+coll = COLLECT(exe,
+               a.binaries,
+               a.zipfiles,
+               a.datas,
+               strip=False,
+               upx=True,
+               name='cellxgene')

makefile

@@ -1,7 +1,7 @@
 BUILDDIR := build
 CLIENTBUILD := $(BUILDDIR)/client
 SERVERBUILD := $(BUILDDIR)/server
-CLEANFILES :=  $(BUILDDIR)/ client/build dist cellxgene.egg-info
+CLEANFILES :=  $(BUILDDIR)/ client/build build dist cellxgene.egg-info
 
 PART ?= patch
 
@@ -84,6 +84,9 @@ release-directly-to-prod : dev-env pydist twine-prod
 dev-env :
 	pip install -r server/requirements-dev.txt
 
+gui-env : dev-env
+	pip install -r server/requirements-gui.txt
+
 # give PART=[major, minor, part] as param to make bump
 bump :
 	bumpversion --config-file .bumpversion.cfg $(PART)
@@ -136,4 +139,21 @@ uninstall :
 build-assets :
 	pyside2-rcc server/gui/cellxgene.qrc -o server/gui/cellxgene_rc.py
 
-.PHONY : build-assets
+gui-spec-osx : clean-lite gui-env
+	pip install -e .[gui]
+	pyi-makespec -D -w --additional-hooks-dir server/gui/ -n cellxgene  --add-binary='/System/Library/Frameworks/Tk.framework/Tk':'tk' --add-binary='/System/Library/Frameworks/Tcl.framework/Tcl':'tcl'  --add-data server/app/web/templates/:server/app/web/templates/ --add-data server/app/web/static/:server/app/web/static/ --icon server/gui/images/cxg_icons.icns server/gui/main.py
+	mv cellxgene.spec cellxgene-osx.spec
+
+gui-spec-windows : clean-lite dev-env
+	pip install -e .[gui]
+	pyi-makespec -D -w --additional-hooks-dir server/gui/ -n cellxgene --add-data server/app/web/templates;server/app/web/templates --add-data server/app/web/static;server/app/web/static --icon server/gui/images/icon.ico server/gui/main.py
+	mv cellxgene.spec cellxgene-windows.spec
+
+gui-build-osx : clean-lite
+	pyinstaller --clean cellxgene-osx.spec
+
+gui-build-windows : clean-lite
+	pyinstaller --clean cellxgene-windows.spec
+
+.PHONY : build-assets gui-build-osx gui-build-windows gui-build-osx gui-build-windows
+

server/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.10.1"

server/app/rest_api/rest.py

@@ -1,9 +1,10 @@
 from http import HTTPStatus
-import pkg_resources
 import warnings
 
 from flask import Blueprint, current_app, jsonify, make_response, request
 from flask_restful import Api, Resource
+from server import __version__ as cellxgene_version
+from anndata import __version__ as anndata_version
 
 from server.app.util.constants import (
     Axis,
@@ -59,16 +60,15 @@ class ConfigAPI(Resource):
                     },
                 ],
                 "displayNames": {
-                    "engine": f"cellxgene Scanpy engine version {pkg_resources.get_distribution('cellxgene').version}",
+                    "engine": f"cellxgene Scanpy engine version ",
                     "dataset": current_app.config["DATASET_TITLE"],
                 },
                 "parameters": {
                     "max-category-items": current_app.data.config["max_category_items"]
                 },
                 "library_versions": {
-                    "scanpy": pkg_resources.get_distribution("scanpy").version,
-                    "cellxgene": pkg_resources.get_distribution("cellxgene").version,
-                    "anndata": pkg_resources.get_distribution("cellxgene").version
+                    "cellxgene": cellxgene_version,
+                    "anndata": anndata_version
                 }
             }
         }

server/gui/cellxgene.spec

@@ -0,0 +1,29 @@
+# -*- mode: python -*-
+
+block_cipher = None
+
+
+a = Analysis(['main.py'],
+             pathex=['/Users/charlotteweaver/Documents/Git/cellxgene/server/gui'],
+             hookspath=["/Users/charlotteweaver/Documents/Git/cellxgene/server/gui/"],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher,
+             noarchive=False)
+
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+
+exe = EXE(pyz,
+          a.scripts,
+          a.binaries,
+          a.zipfiles,
+          a.datas,
+          [],
+          name='cellxgene',
+          debug=False,
+          bootloader_ignore_signals=False,
+          strip=False,
+          upx=True,
+          runtime_tmpdir=None,
+          console=True )

server/gui/hook-cefpython3.py

@@ -0,0 +1,237 @@
+"""
+This is PyInstaller hook file for CEF Python. This file
+helps PyInstaller find CEF Python dependencies that are
+required to run final executable.
+
+See PyInstaller docs for hooks:
+https://pyinstaller.readthedocs.io/en/stable/hooks.html
+"""
+
+import glob
+import os
+import platform
+import re
+import sys
+import PyInstaller
+from PyInstaller.utils.hooks import is_module_satisfies, get_package_paths
+from PyInstaller.compat import is_win, is_darwin, is_linux, is_py2
+from PyInstaller import log as logging
+
+# Constants
+CEFPYTHON_MIN_VERSION = "57.0"
+PYINSTALLER_MIN_VERSION = "3.2.1"
+
+# Makes assumption that using "python.exe" and not "pyinstaller.exe"
+# TODO: use this code to work cross-platform:
+# from PyInstaller.utils.hooks import get_package_paths
+# get_package_paths("cefpython3")
+
+CEFPYTHON3_DIR = get_package_paths("cefpython3")[1]
+
+CYTHON_MODULE_EXT = ".pyd" if is_win else ".so"
+
+# Globals
+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.")
+
+
+def check_pyinstaller_version():
+    """Using is_module_satisfies() for pyinstaller fails when
+    installed using 'pip install develop.zip' command
+    (PyInstaller Issue #2802)."""
+    # Example version string for dev version of pyinstaller:
+    # > 3.3.dev0+g5dc9557c
+    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)
+
+
+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)
+
+
+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))
+    assert len(pyds) > 1, "Missing cefpython3 Cython modules"
+    modules = []
+    for path in pyds:
+        filename = os.path.basename(path)
+        mod = filename.replace(CYTHON_MODULE_EXT, "")
+        modules.append(mod)
+    return modules
+
+
+def get_excluded_cefpython_modules():
+    """CEF Python package includes Cython modules for various Python
+       versions. When using Python 2.7 pyinstaller should not
+       bundle modules for eg. Python 3.6, otherwise it will
+       cause to include Python 3 dll dependencies. Returns a list
+       of fully qualified names eg. 'cefpython3.cefpython_py27'."""
+    pyver = "".join(map(str, sys.version_info[:2]))
+    pyver_string = "py%s" % pyver
+    modules = get_cefpython_modules()
+    excluded = []
+    for mod in modules:
+        if pyver_string in mod:
+            continue
+        excluded.append("cefpython3.%s" % mod)
+        logger.info("Exclude cefpython3 module: %s" % excluded[-1])
+    return excluded
+
+
+def get_cefpython3_datas():
+    """Returning almost all of cefpython binaries as DATAS (see exception
+    below), because pyinstaller does strange things and fails if these are
+    returned as BINARIES. It first updates manifest in .dll files:
+    >> Updating manifest in chrome_elf.dll
+
+    And then because of that it fails to load the library:
+    >> hsrc = win32api.LoadLibraryEx(filename, 0, LOAD_LIBRARY_AS_DATAFILE)
+    >> pywintypes.error: (5, 'LoadLibraryEx', 'Access is denied.')
+
+    It is not required for pyinstaller to modify in any way
+    CEF binaries or to look for its dependencies. CEF binaries
+    does not have any external dependencies like MSVCR or similar.
+
+    The .pak .dat and .bin files cannot be marked as BINARIES
+    as pyinstaller would fail to find binary depdendencies on
+    these files.
+
+    One exception is subprocess (subprocess.exe on Windows) executable
+    file, which is passed to pyinstaller as BINARIES in order to collect
+    its dependecies.
+
+    DATAS are in format: tuple(full_path, dest_subdir).
+    """
+    ret = list()
+
+    if is_win:
+        cefdatadir = "."
+    elif is_darwin or is_linux:
+        cefdatadir = "."
+    else:
+        assert False, "Unsupported system {}".format(platform.system())
+
+    # Binaries, licenses and readmes in the cefpython3/ directory
+    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():
+            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"):
+            logger.info("Include cefpython3 data: {}".format(filename))
+            ret.append((os.path.join(CEFPYTHON3_DIR, filename), cefdatadir))
+
+    if is_darwin:
+        # "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")
+        base_path = os.path.join(CEFPYTHON3_DIR, 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)
+                dest_path = os.path.relpath(path, CEFPYTHON3_DIR)
+                ret.append((absolute_file_path, dest_path))
+                logger.info("Include cefpython3 data: {}/{}".format(dest_path, file))
+    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"
+        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")))
+
+        # 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")))
+    return ret
+
+
+# ----------------------------------------------------------------------------
+# Main
+# ----------------------------------------------------------------------------
+
+# Checks
+check_platforms()
+check_pyinstaller_version()
+check_cefpython3_version()
+
+# Info
+logger.info("CEF Python package directory: %s" % CEFPYTHON3_DIR)
+
+# Hidden imports.
+# PyInstaller has no way on detecting imports made by Cython
+# modules, so all pure Python imports made in cefpython .pyx
+# files need to be manually entered here.
+# TODO: Write a tool script that would find such imports in
+#       .pyx files automatically.
+hiddenimports = [
+    "codecs",
+    "copy",
+    "datetime",
+    "inspect",
+    "json",
+    "os",
+    "platform",
+    "random",
+    "re",
+    "sys",
+    "time",
+    "traceback",
+    "types",
+    "urllib",
+    "weakref",
+]
+if is_py2:
+    hiddenimports += [
+        "urlparse",
+    ]
+
+# Excluded modules
+excludedimports = get_excluded_cefpython_modules()
+
+# Include binaries requiring to collect its dependencies
+if is_darwin or is_linux:
+    binaries = [(os.path.join(CEFPYTHON3_DIR, "subprocess"), ".")]
+elif is_win:
+    binaries = [(os.path.join(CEFPYTHON3_DIR, "subprocess.exe"), ".")]
+else:
+    binaries = []
+
+# Include datas
+datas = get_cefpython3_datas()
+
+# Notify pyinstaller.spec code that this hook was executed
+# and that it succeeded.
+os.environ["PYINSTALLER_CEFPYTHON3_HOOK_SUCCEEDED"] = "1"

server/gui/main.py

@@ -1,6 +1,6 @@
 # flake8: noqa F403, F405
 from functools import partialmethod
-from multiprocessing import Pipe, Process
+from multiprocessing import Pipe, Process, freeze_support
 from os import environ
 from os.path import splitext, basename, dirname, join
 import sys
@@ -172,7 +172,7 @@ class LoadWidget(QFrame):
         # UI section
         # TODO add cancel button to send back to browser (if available)
 
-        self.file_area = FileArea()
+        self.file_area = FileArea(self)
         self.file_name.signals.changed.connect(self.updatePath)
 
         self.launch_widget = QLabel("Select a file to launch cellxgene")
@@ -301,7 +301,7 @@ class FilePath(QObject):
 
 
 class FileArea(QFrame):
-    def __init__(self):
+    def __init__(self, parent):
         super(FileArea, self).__init__()
         self.setFrameShape(QFrame.Box)
         self.setMinimumHeight(100)
@@ -357,6 +357,7 @@ class FileArea(QFrame):
 
 
 def main():
+    freeze_support()
     # This generates an error.log file on error
     sys.excepthook = cef.ExceptHook  # To shutdown all CEF processes on error
     settings = {}

server/requirements-gui.txt

@@ -0,0 +1,4 @@
+cefpython3>=66
+requests
+PyInstaller>=3.4
+PySide2>=5.12.3