Merge pull request #84 from nel-lab/master

lots-of-stuff <- master

environment.yml

@@ -4,7 +4,5 @@ dependencies:
  - caiman >= 1.9.10
  - pandas
  - requests
- - qtpy
- - pyqt
  - click
 

mesmerize_core/__init__.py

@@ -1,6 +1,5 @@
 from .batch_utils import (
  COMPUTE_BACKENDS,
- COMPUTE_BACKEND_QPROCESS,
  COMPUTE_BACKEND_SLURM,
  COMPUTE_BACKEND_SUBPROCESS,
  set_parent_raw_data_path,
@@ -14,7 +13,6 @@
 
 __all__ = [
  "COMPUTE_BACKENDS",
- "COMPUTE_BACKEND_QPROCESS",
  "COMPUTE_BACKEND_SLURM",
  "COMPUTE_BACKEND_SUBPROCESS",
  "set_parent_raw_data_path",

mesmerize_core/batch_utils.py

@@ -17,23 +17,12 @@
  "cnmfe": cnmfe,
 }
 
-try:
- import PyQt5
-
- HAS_PYQT = True
-except ImportError:
- HAS_PYQT = False
-
-COMPUTE_BACKEND_QPROCESS = "qprocess" #: QProcess backend for use in napari
-COMPUTE_BACKEND_SUBPROCESS = "subprocess" #: subprocess backend, for use output a Qt application such as a notebook
+COMPUTE_BACKEND_SUBPROCESS = "subprocess" #: subprocess backend
 COMPUTE_BACKEND_SLURM = "slurm" #: SLURM backend, not yet implemented
 
 COMPUTE_BACKENDS = [COMPUTE_BACKEND_SUBPROCESS, COMPUTE_BACKEND_SLURM]
 
-if HAS_PYQT:
- COMPUTE_BACKENDS += [COMPUTE_BACKEND_QPROCESS]
-
-DATAFRAME_COLUMNS = ["algo", "name", "input_movie_path", "params", "outputs", "uuid"]
+DATAFRAME_COLUMNS = ["algo", "name", "input_movie_path", "params", "outputs", "comments", "uuid"]
 
 
 def set_parent_raw_data_path(path: Union[Path, str]) -> Path:

mesmerize_core/caiman_extensions/common.py

@@ -16,12 +16,8 @@
  get_parent_raw_data_path,
  PathsDataFrameExtension,
  PathsSeriesExtension,
- HAS_PYQT,
 )
 from ..utils import validate_path, IS_WINDOWS, make_runfile, warning_experimental
-
-if HAS_PYQT:
- from PyQt5 import QtCore
 from caiman import load_memmap
 
 
@@ -108,6 +104,7 @@ def add_item(self, algo: str, name: str, input_movie_path: str, params: dict):
  "input_movie_path": str(input_movie_path),
  "params": params,
  "outputs": None, # to store dict of output information, such as output file paths
+ "comments": None,
  "uuid": str(
  uuid4()
  ), # unique identifier for this combination of movie + params
@@ -137,42 +134,7 @@ class CaimanSeriesExtensions:
 
  def __init__(self, s: pd.Series):
  self._series = s
- self.process: [Union, QtCore.QProcess, Popen] = None
-
- def _run_qprocess(
- self,
- runfile_path: str,
- callbacks_finished: List[callable],
- callback_std_out: Optional[callable] = None,
- ) -> QtCore.QProcess:
-
- # Create a QProcess
- self.process = QtCore.QProcess()
- self.process.setProcessChannelMode(QtCore.QProcess.MergedChannels)
-
- # Set the callback function to read the stdout
- if callback_std_out is not None:
- self.process.readyReadStandardOutput.connect(
- partial(callback_std_out, self.process)
- )
-
- # connect the callback functions for when the process finishes
- if callbacks_finished is not None:
- for f in callbacks_finished:
- self.process.finished.connect(f)
-
- parent_path = self._series.paths.resolve(self._series.input_movie_path).parent
-
- # Set working dir for the external process
- self.process.setWorkingDirectory(str(parent_path))
-
- # Start the external process
- if IS_WINDOWS:
- self.process.start("powershell.exe", [runfile_path])
- else:
- self.process.start(runfile_path)
-
- return self.process
+ self.process: Popen = None
 
  def _run_subprocess(
  self,