Restructuring code base for `Sequence` and attached classes - #119

Merged

DaniBodor merged 204 commits into

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181_refactor_sequence_psomhorst

Mar 11, 2024

Commits on Nov 14, 2023

Commits on Nov 15, 2023

Remove single-use method for simplicity
psomhorst
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e9abfb9
Raise when checking equivalence
psomhorst
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e4b1536
Add events and phases to DraegerEITData object when loading
psomhorst
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44bfb9c
Change framerate to float instead of int
psomhorst
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f474a3f
Select class explicitly when concatenating, mainly for type checking
psomhorst
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0d8e442
Improve type checking in EITData.check_equivalence()
psomhorst
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2d33a17
Use own PathLike, not os version
psomhorst
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159d686
Add comment explaining why @override is used
psomhorst
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6c922de
Remove timing error class
psomhorst
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4b167b7
Add to and rewrite data loading in TimpelEITData
psomhorst
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818c0a8
Remove unused imports
psomhorst
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b1723cb
Add comments disabling linting errors
psomhorst
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3aa791f
Removed unused label argument
psomhorst
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b2ffa05
Remove unused imports
psomhorst
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1dc96e7
Update `check_equivalence` and `__eq__` methods
psomhorst
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5955cdc
Update `concatenate` method
psomhorst
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228557f

Commits on Nov 17, 2023

Create TypeAlias using Union instead of |
psomhorst
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12f5847
Add medibus data parsing to DraegerEITData.from_path()
psomhorst
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b55851a
Add ContinuousData and variant and collection
psomhorst
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3460681
Add boilerplate for SparseData and and collection
psomhorst
committed
3af9a23
Remove outdated mentioning of waveform data
psomhorst
committed
88eb00f
Fix name of pixel_impendace
psomhorst
committed
eaf1e52
Fix linting issues
psomhorst
committed
ab90303

Commits on Nov 20, 2023

Remove unused typevar
psomhorst
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4a6b2b8
Improve VariantCollection variant_type type hinting
psomhorst
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cb886dc

Commits on Nov 21, 2023

Fix linting issues
psomhorst
committed
dc9160a
Replace complex try/except statement with `contextlib.suppress()`
psomhorst
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d1c0163

Commits on Nov 24, 2023

Commits on Nov 28, 2023

implemented _from_path method for parsing sentec data
wbaccinelli
committed
62cc36e
added warnings for data length
wbaccinelli
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6c9ea9e

Commits on Nov 30, 2023

create folder structure for all mixins
Dani Bodor
committed
d2ddce8
refactor slicing mixin
Dani Bodor
committed
7806dfe

Commits on Dec 1, 2023

using reader
wbaccinelli
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e88a618
improving code structure
wbaccinelli
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2bf314c
reformatting with black
wbaccinelli
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440d666
moved endiness to Reader contructor arguments
wbaccinelli
committed
ef7d8fc

Commits on Dec 6, 2023

force expected slicing inclusion behavior
Dani Bodor
committed
faf345b
fix labeling
Dani Bodor
committed
c91f366
start of slicing test
Dani Bodor
committed
7e9d379
make slice by time result in expected behavior
Dani Bodor
committed
a4515dd
changed naming convention
wbaccinelli
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3541055
added warning for frameset read from file
wbaccinelli
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d06efb1
Update eitprocessing/eit_data/sentec.py

wbaccinelli
and
psomhorst
authored
c201fdb

Commits on Dec 8, 2023

docs: add code documentation to slicing module
Dani Bodor
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b44c974
bisect left on end_inclusive
Dani Bodor
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6dc006b
Merge pull request #132 from EIT-ALIVE/129a_slicing_mixin_dbodor
Dani Bodor
authored
5ae7437
reading data for version 1
wbaccinelli
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529be4d
reading timestamp from TimeOfCaptuer
wbaccinelli
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3124ff5
optimized times
wbaccinelli
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17cc844
time starting from zero and converted to seconds
wbaccinelli
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b6e4663

Commits on Jan 24, 2024

Commits on Jan 31, 2024

implemented _from_path method for parsing sentec data
wbaccinelli
committed
e08089b
added warnings for data length
wbaccinelli
committed
957d395
using reader
wbaccinelli
committed
e155f08
improving code structure
wbaccinelli
committed
f9f3c9a
reformatting with black
wbaccinelli
committed
0c30aaf
moved endiness to Reader contructor arguments
wbaccinelli
committed
0c568bd
changed naming convention
wbaccinelli
committed
21a5740
added warning for frameset read from file
wbaccinelli
committed
284be14
Update eitprocessing/eit_data/sentec.py

wbaccinelli
and
psomhorst
committed
5c2695f
reading data for version 1
wbaccinelli
committed
1452c87
reading timestamp from TimeOfCaptuer
wbaccinelli
committed
9e110a2
optimized times
wbaccinelli
committed
b4ae630
time starting from zero and converted to seconds
wbaccinelli
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3d28266
time wrapping
wbaccinelli
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2da2298
using mmap
wbaccinelli
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4917e84
Merge branch '92_read_sentec_data_wbaccinelli' of https://github.com/EIT-ALIVE/eitprocessing into 92_read_sentec_data_wbaccinelli
wbaccinelli
committed
1a9375b

Commits on Feb 2, 2024

Commits on Feb 5, 2024

docs: improve documentation for slicing mixin
Dani Bodor
committed
7c632d2
feature: create generic equality function
Dani Bodor
committed
c9e03b7
feature: create generic check equivalence method
Dani Bodor
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cd55a45
refactor: use generic equality and equivalence functions throughout
Dani Bodor
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d8b2611
test: create dummy test scripts for equality
Dani Bodor
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fee1ddf
Merge pull request #133 from EIT-ALIVE/129b_eq_dbodor
Dani Bodor
authored
2617164

Commits on Feb 14, 2024

plot with multiple axis
wbaccinelli
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03a96cf

Commits on Feb 20, 2024

docs: remove module level docstrings
Dani Bodor
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326f434
style: add ruff settings to pyproject.toml
Dani Bodor
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19d8f60
style: auto format settings
Dani Bodor
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77a02c7
docs: update dev readme to ruff
Dani Bodor
committed
7769b3e

Commits on Feb 23, 2024

Merge pull request #144 from EIT-ALIVE/143_ruff_linter_formatter_dbodor
Dani Bodor
authored
2e96515
Add ignore codes for ruff
psomhorst
committed
b5607f7
Merge pull request #146 from EIT-ALIVE/hotfix/add_ruff_ignore_codes
Dani Bodor
authored
3057acd
Merge branch '181_refactor_sequence_psomhorst' of https://github.com/EIT-ALIVE/eitprocessing into 181_refactor_sequence_psomhorst
wbaccinelli
committed
80204c6
hotifix medibut category
wbaccinelli
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20d6165
Merge pull request #147 from EIT-ALIVE/hotfix_medibus_category_wbaccinelli
Dani Bodor
authored
2d10494
docs: add project descriptors to pyproject.toml
Dani Bodor
committed
5689f54
build: add dependencies to pyproject.toml
Dani Bodor
committed
989419a
build: setuptools settings
Dani Bodor
committed
251182d
annotate setup.cfg
Dani Bodor
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f5a1871
build: delete setup.cfg and setup.py
Dani Bodor
committed
d3e4d6e
Merge pull request #149 from EIT-ALIVE/148_installationfiles_dbodor
Dani Bodor
authored
c68c325
CI uses ruff instead of
Dani Bodor
committed
ffa7b47
Merge pull request #150 from EIT-ALIVE/143b_ruff_on_CI_dbodor
Dani Bodor
authored
f65f612
Remove methods in preparation for mixin classes and remove custom exceptions
psomhorst
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8c69556
Rename methods and arguments for better consistency
psomhorst
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3a21bf6
Remove merge ContinuousData and ContinuousDataVariant, removing the latter
psomhorst
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7bac1a7
Rename `calculated_from` to `derived_from`
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834b099
Add category attribute to ContinuousData
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8c0ed64
Add copy and derive methods to ContinuousData
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a81636a
Add lock and unlock methods, and locker property to ContinuousData
psomhorst
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260e9ad
Fix issue returning on the first added ContinousData object
psomhorst
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93a63f0
Add helper methods
psomhorst
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24d2522
Update DraegerEITData.from_path to reflect removal of ContinuousDataVariant
psomhorst
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a95f3fa
Update type hints
psomhorst
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2a36117
Apply Ruff linting and formatting
psomhorst
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a24446e
Move ContinuousDataCollection to data_collection
psomhorst
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1c6e48c
Generalize DataCollection for use with a any data
psomhorst
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5816c8c
Improve type hinting
psomhorst
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fff97fc
Pass `**kwargs` to function when deriving
psomhorst
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be1bae7
Remove ContinuousDataCollection and SparseDataCollection from EITData
psomhorst
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d656d38
Ruff formatting and linting
psomhorst
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745bf01
Set sequence attributes to DataCollections
psomhorst
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6516769
Ruff linting and formatting
psomhorst
committed
4cf006a
Ruff linting and formatting
psomhorst
committed
956cccc
Ruff linting and formatting
psomhorst
committed
cb712a1
Implement slicing mixin in sequence
psomhorst
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90b7ae0
Add Equivalenca and concatenate to DataCollection
psomhorst
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22f341f
Remove Variants and replace with DataCollections
psomhorst
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eef12c6
Fix instance check
psomhorst
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33ab6e4
Remove NoVendorProvided error
psomhorst
committed
30ea158
Update class selection
psomhorst
committed
c014315
Fix linting issues
psomhorst
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8aca80a
.
psomhorst
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22c0c71
Fix Self import
psomhorst
committed
8e7d5a0
Update MedibusField definition
psomhorst
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7091ba1
Update tests
psomhorst
committed
c2a860b
Fix initialization of DataCollection
psomhorst
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fcd9b13
Fix erroneous Self import
psomhorst
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e21f527
Replace name in DataCollection with label
psomhorst
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4dec8d0
Improve type hinting
psomhorst
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c32070d
Fix return type to DataCollection
psomhorst
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e669030
Make concatenate a normal instance method, also callable also class method
psomhorst
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baf7a7e
Fix return type of DraegerEITData.from_path()
psomhorst
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37a58e3
Fix equality __eq__ method for dicts
psomhorst
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02fbb31
Remove label alterations
psomhorst
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405ae9a
Remove label from Sequence
psomhorst
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d8e276f
Add time property and __len__ method to Sequence
psomhorst
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f315474
Fix DataCollection factories
psomhorst
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ca349ec
User proper concatenate function
psomhorst
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d9151e5
Fix slicing of Sequence
psomhorst
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fc4b6cf
Add numpy to Sequence
psomhorst
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ee6e006
Update most tests for Sequence
psomhorst
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4ce327a

Commits on Feb 29, 2024

equality function also checks for same number of arguments
Dani Bodor
committed
a0cf113
start linting
Dani Bodor
committed
bd47620
add docstring for `ContinuousData`
Dani Bodor
committed
0192bae

Commits on Mar 4, 2024

Lock data when loaded
psomhorst
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52054eb
Disable replacing locked data
psomhorst
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2958efd
Unlock data after copying
psomhorst
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c96c43b
Update derive to accept arguments for the function and attributes for the derived copy
psomhorst
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4ca6c97
Update docstring
psomhorst
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6e32a0d
Add method docstrings
psomhorst
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7a4ad6c

Commits on Mar 5, 2024

style: absolute imports over relative imports
Dani Bodor
committed
d7a736d
minor changes to comments, error/warning messages, type hints, noqas, zip strictness
Dani Bodor
committed
fa45d33

Commits on Mar 6, 2024

Make ContinuousData.loaded a property instead of an attribute
psomhorst
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15b424e
Add argument to lock(), unlock() methods
psomhorst
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f71d69c
Add time attribute and Equivalence and SelectByTime parent classes
psomhorst
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224a964
Bind generic type to expected data types, warn when initialized with other type
psomhorst
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db055ef
Add docstrings
psomhorst
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4c1cc5f
Add comments about item checks
psomhorst
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dc591a4
Simplify length checks

psomhorst
and
Dani Bodor
authored
1781d94
Fix non-existing classes and replace with DataCollection([...]Data)
psomhorst
committed
aa9d10a
Put type checking assertions behind `if TYPE_CHECKING`.
psomhorst
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b3abe8c
Remove custom PathLike and PathArg type aliases
psomhorst
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8adfcea
Make UnknownVendorError subclass of VendorError

psomhorst
and
Dani Bodor
authored
95454c2
Raise exception when image size is not as expected
psomhorst
committed
af44e2b
Merge pull request #151 from EIT-ALIVE/126b_dbadditions
Dani Bodor
authored
34cc562

Commits on Mar 7, 2024

Add option to pass multiple arguments to `lock()` and `unlock()`
psomhorst
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1b0b10f
Fix TypeVar constraint

psomhorst
and
Dani Bodor
authored
e1c9ce3
Replace warning about unexpected data types with exception

psomhorst
and
Dani Bodor
authored
3d53fb8
Fix linting issues
psomhorst
committed
6be5023
Move imports to prevent circular imports
psomhorst
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a87c671
Shorten type hints
psomhorst
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695c2ab
Replace relative import with absolute import
psomhorst
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11b2b67
Add and improve documentation
psomhorst
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8500a17
Fix linting issues
psomhorst
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354487e
Add docstring for DataCollection._check_item()
psomhorst
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5c6521e
docs: expand docstrings for `lock` and `unlock`
Dani Bodor
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0d24207
docs: remove types from `EITData.from_path` docstring
Dani Bodor
committed
a66c80f
Fix circular import
psomhorst
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b993ef2
Check item type is subclass of constraint, instead of exactly constraint type
psomhorst
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aa6c724
Expand checking for locked attribute to any numpy array
psomhorst
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1c082b2
Merge pull request #142 from EIT-ALIVE/126-create-continuousdata-class
Dani Bodor
authored
ec8d35b

Commits on Mar 8, 2024

add `_sliced_copy` method to continousdata
Dani Bodor
committed
e6a369a
hotfix `_convert_medibus_data`
Dani Bodor
committed
1b86be7
hotfix set attr method
Dani Bodor
committed
8a36244

Commits on Mar 11, 2024

Fix try/except to allow appropriate AttributeError
psomhorst
committed
7351fdf
Add `__len__()` to ContinuousData
psomhorst
committed
a6ded81
Merge pull request #156 from EIT-ALIVE/slicedcopy_continuousdata_suggestions_psomhorst
Dani Bodor
authored
59586ce
Merge pull request #155 from EIT-ALIVE/slicedcopy_continuousdata_dbodor
Dani Bodor
authored
44d3b75
add label, name, and description attributes to Sequence
Dani Bodor
committed
58685fa
update `Sequence` docstring
Dani Bodor
committed
e33f79a
Add label, name, description to _sliced_copy()
psomhorst
committed
45023ad
Merge pull request #158 from EIT-ALIVE/sequence_labels_dbodor
Dani Bodor
authored
7e60cbf