From cdf2e652c2e4ea87b253cbf6ca9b6fbb723dc7a2 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Tue, 29 Nov 2022 14:49:28 -0800 Subject: [PATCH 01/13] Update for 3.10 --- FlowCytometryTools/core/bases.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index 3d7b7e4..ec7d2c8 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -368,6 +368,14 @@ def apply(self, func, applyto="measurement", noneval=nan, setdata=False): Well = Measurement +import collections +try: + from collections import abc + collections.MutableMapping = abc.MutableMapping + collections.Iterable = abc.Iterable + collections.Mapping = abc.Mapping +except: + pass class MeasurementCollection(abc.MutableMapping, BaseObject): From d363b278c94396ee6c44fc0f43e1640bdeb9d0af Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Fri, 9 Dec 2022 11:34:20 -0800 Subject: [PATCH 02/13] Fix --- FlowCytometryTools/core/containers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/FlowCytometryTools/core/containers.py b/FlowCytometryTools/core/containers.py index c33c437..9f6817b 100644 --- a/FlowCytometryTools/core/containers.py +++ b/FlowCytometryTools/core/containers.py @@ -132,11 +132,11 @@ def plot( plot_output = graph.plotFCM(self.data, channel_names, kind=kind, **kwargs) if gates is not None: + if gate_colors is None: gate_colors = cycle(("b", "g", "r", "m", "c", "y")) - if not isinstance(gate_lw, collections.Iterable): - gate_lw = [gate_lw] + gate_lw = [gate_lw] gate_lw = cycle(gate_lw) From 3efacafa927057f78867692ac06c25f7e2f5b743 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 14:32:12 -0700 Subject: [PATCH 03/13] Fix' --- FlowCytometryTools/core/bases.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index ec7d2c8..1a722d5 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -97,7 +97,7 @@ def queueable(fun, *args, **kwargs): '"%s" must be a parameter of queued function "%s"' % (_now, fun.__name__) ) f_name = fun.__name__ - kw_name = inspect.getargspec(fun).keywords + kw_name = inspect.getarg(fun).keywords kws = params.pop(kw_name, {}) params.update(kws) if params[_now]: From 55ffb71af086fbc1859ec9e8a2c3945e81db7a2e Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 14:37:41 -0700 Subject: [PATCH 04/13] Fix2 --- FlowCytometryTools/core/bases.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index 1a722d5..b037cfa 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -97,7 +97,7 @@ def queueable(fun, *args, **kwargs): '"%s" must be a parameter of queued function "%s"' % (_now, fun.__name__) ) f_name = fun.__name__ - kw_name = inspect.getarg(fun).keywords + kw_name = inspect.getargs(fun).keywords kws = params.pop(kw_name, {}) params.update(kws) if params[_now]: From 830fb388689768ffde05e83b9e0743f09514fa55 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 14:44:08 -0700 Subject: [PATCH 05/13] Fix3 --- FlowCytometryTools/core/bases.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index b037cfa..1925ad4 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -97,7 +97,7 @@ def queueable(fun, *args, **kwargs): '"%s" must be a parameter of queued function "%s"' % (_now, fun.__name__) ) f_name = fun.__name__ - kw_name = inspect.getargs(fun).keywords + kw_name = inspect.getfullargspec(fun).keywords kws = params.pop(kw_name, {}) params.update(kws) if params[_now]: From d52968d4c1bae920d8cd99e88b661ab8f86f95f7 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:15:07 -0700 Subject: [PATCH 06/13] TryThis --- FlowCytometryTools/core/bases.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index 1925ad4..a041f36 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -97,7 +97,10 @@ def queueable(fun, *args, **kwargs): '"%s" must be a parameter of queued function "%s"' % (_now, fun.__name__) ) f_name = fun.__name__ - kw_name = inspect.getfullargspec(fun).keywords + print(fun) + print(type(fun)) + kw_name = inspect.getfullargspec(fun) + print(kw_name) kws = params.pop(kw_name, {}) params.update(kws) if params[_now]: From 38d8b6c589f25cf92e5021874d7ef34f2ef3de55 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:18:47 -0700 Subject: [PATCH 07/13] Try this --- FlowCytometryTools/core/bases.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index a041f36..e6b51c3 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -99,7 +99,7 @@ def queueable(fun, *args, **kwargs): f_name = fun.__name__ print(fun) print(type(fun)) - kw_name = inspect.getfullargspec(fun) + kw_name = inspect.getfullargspec(fun).varkw print(kw_name) kws = params.pop(kw_name, {}) params.update(kws) From 9e8d76a6b7651b1054266074087daf21c4a7b572 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:34:54 -0700 Subject: [PATCH 08/13] Try this 2 --- FlowCytometryTools/core/bases.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index e6b51c3..42772ba 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -99,7 +99,7 @@ def queueable(fun, *args, **kwargs): f_name = fun.__name__ print(fun) print(type(fun)) - kw_name = inspect.getfullargspec(fun).varkw + kw_name = inspect.getfullargspec(fun).kwonlyargs print(kw_name) kws = params.pop(kw_name, {}) params.update(kws) From 6c26a878c8272e7bbff317ad84c703de28883265 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:41:53 -0700 Subject: [PATCH 09/13] Try this 2 --- FlowCytometryTools/core/bases.py | 2 +- FlowCytometryTools/core/containers.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index 42772ba..9492ba0 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -99,7 +99,7 @@ def queueable(fun, *args, **kwargs): f_name = fun.__name__ print(fun) print(type(fun)) - kw_name = inspect.getfullargspec(fun).kwonlyargs + kw_name = inspect.getfullargspec(fun).varkws print(kw_name) kws = params.pop(kw_name, {}) params.update(kws) diff --git a/FlowCytometryTools/core/containers.py b/FlowCytometryTools/core/containers.py index 9f6817b..6f3a29d 100644 --- a/FlowCytometryTools/core/containers.py +++ b/FlowCytometryTools/core/containers.py @@ -285,6 +285,7 @@ def transform( for i, r in channel_meta.iterrows() if self.channel_names[i - 1] in channels ] + print(ranges) if not np.allclose(ranges, ranges[0]): raise Exception( """Not all specified channels have the same data range, From de41a826f30ba799008504ea2c146657691927f4 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:42:29 -0700 Subject: [PATCH 10/13] Try this 4 --- FlowCytometryTools/core/bases.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index 9492ba0..5fe1115 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -97,10 +97,7 @@ def queueable(fun, *args, **kwargs): '"%s" must be a parameter of queued function "%s"' % (_now, fun.__name__) ) f_name = fun.__name__ - print(fun) - print(type(fun)) - kw_name = inspect.getfullargspec(fun).varkws - print(kw_name) + kw_name = inspect.getfullargspec(fun).varkw kws = params.pop(kw_name, {}) params.update(kws) if params[_now]: From c98e227da9dc3ce89ffe196c0b7aea370d304b93 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:44:05 -0700 Subject: [PATCH 11/13] Try this 4 --- FlowCytometryTools/core/containers.py | 1 + 1 file changed, 1 insertion(+) diff --git a/FlowCytometryTools/core/containers.py b/FlowCytometryTools/core/containers.py index 6f3a29d..4b5823a 100644 --- a/FlowCytometryTools/core/containers.py +++ b/FlowCytometryTools/core/containers.py @@ -286,6 +286,7 @@ def transform( if self.channel_names[i - 1] in channels ] print(ranges) + print(channels) if not np.allclose(ranges, ranges[0]): raise Exception( """Not all specified channels have the same data range, From 49b2f9464068fa8c8e7d2947853cc779ab5d6f53 Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 15:46:04 -0700 Subject: [PATCH 12/13] Debug --- FlowCytometryTools/core/bases.py | 1 + 1 file changed, 1 insertion(+) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index 5fe1115..ea5692b 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -91,6 +91,7 @@ def int2letters(x, alphabet): @decorator.decorator def queueable(fun, *args, **kwargs): + print(fun, *args, **kwargs) params = inspect.getcallargs(fun, *args, **kwargs) if not _now in params: raise ValueError( From 4a48da2020d17927ac418e7694f66f4b94c1f59e Mon Sep 17 00:00:00 2001 From: Brian Orcutt-Jahns Date: Thu, 27 Apr 2023 16:39:07 -0700 Subject: [PATCH 13/13] Fixed --- FlowCytometryTools/core/bases.py | 1 - FlowCytometryTools/core/containers.py | 2 -- 2 files changed, 3 deletions(-) diff --git a/FlowCytometryTools/core/bases.py b/FlowCytometryTools/core/bases.py index ea5692b..5fe1115 100644 --- a/FlowCytometryTools/core/bases.py +++ b/FlowCytometryTools/core/bases.py @@ -91,7 +91,6 @@ def int2letters(x, alphabet): @decorator.decorator def queueable(fun, *args, **kwargs): - print(fun, *args, **kwargs) params = inspect.getcallargs(fun, *args, **kwargs) if not _now in params: raise ValueError( diff --git a/FlowCytometryTools/core/containers.py b/FlowCytometryTools/core/containers.py index 4b5823a..9f6817b 100644 --- a/FlowCytometryTools/core/containers.py +++ b/FlowCytometryTools/core/containers.py @@ -285,8 +285,6 @@ def transform( for i, r in channel_meta.iterrows() if self.channel_names[i - 1] in channels ] - print(ranges) - print(channels) if not np.allclose(ranges, ranges[0]): raise Exception( """Not all specified channels have the same data range,