pyPTE 1.0.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (15) hide show
  1. pypte-1.0.0/.gitignore +186 -0
  2. pypte-1.0.0/CHANGELOG.md +163 -0
  3. pypte-1.0.0/LICENSE +674 -0
  4. pypte-1.0.0/PKG-INFO +103 -0
  5. pypte-1.0.0/README.md +72 -0
  6. pypte-1.0.0/pyPTE/__init__.py +5 -0
  7. pypte-1.0.0/pyPTE/adapters/__init__.py +0 -0
  8. pypte-1.0.0/pyPTE/adapters/mne_adapter.py +67 -0
  9. pypte-1.0.0/pyPTE/adapters/pandas_adapter.py +29 -0
  10. pypte-1.0.0/pyPTE/core/__init__.py +1 -0
  11. pypte-1.0.0/pyPTE/core/handle_multi.py +52 -0
  12. pypte-1.0.0/pyPTE/core/pyPTE.py +268 -0
  13. pypte-1.0.0/pyPTE/py.typed +0 -0
  14. pypte-1.0.0/pyproject.toml +106 -0
  15. pypte-1.0.0/tests/test_pyPTE.py +226 -0
pypte-1.0.0/.gitignore ADDED
@@ -0,0 +1,186 @@
1
+ reated by https://www.gitignore.io/api/linux,python,pycharm+all
2
+
3
+ ### Linux ###
4
+ *~
5
+
6
+ # temporary files which can be created if a process still has a handle open of a deleted file
7
+ .fuse_hidden*
8
+
9
+ # KDE directory preferences
10
+ .directory
11
+
12
+ # Linux trash folder which might appear on any partition or disk
13
+ .Trash-*
14
+
15
+ # .nfs files are created when an open file is removed but is still being accessed
16
+ .nfs*
17
+
18
+ ### PyCharm+all ###
19
+ # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
20
+ # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
21
+
22
+ # User-specific stuff:
23
+ .idea/**/workspace.xml
24
+ .idea/**/tasks.xml
25
+ .idea/dictionaries
26
+
27
+ # Sensitive or high-churn files:
28
+ .idea/**/dataSources/
29
+ .idea/**/dataSources.ids
30
+ .idea/**/dataSources.xml
31
+ .idea/**/dataSources.local.xml
32
+ .idea/**/sqlDataSources.xml
33
+ .idea/**/dynamic.xml
34
+ .idea/**/uiDesigner.xml
35
+
36
+ # Gradle:
37
+ .idea/**/gradle.xml
38
+ .idea/**/libraries
39
+
40
+ # CMake
41
+ cmake-build-debug/
42
+
43
+ # Mongo Explorer plugin:
44
+ .idea/**/mongoSettings.xml
45
+
46
+ ## File-based project format:
47
+ *.iws
48
+
49
+ ## Plugin-specific files:
50
+
51
+ # IntelliJ
52
+ /out/
53
+
54
+ # mpeltonen/sbt-idea plugin
55
+ .idea_modules/
56
+
57
+ # JIRA plugin
58
+ atlassian-ide-plugin.xml
59
+
60
+ # Cursive Clojure plugin
61
+ .idea/replstate.xml
62
+
63
+ # Ruby plugin and RubyMine
64
+ /.rakeTasks
65
+
66
+ # Crashlytics plugin (for Android Studio and IntelliJ)
67
+ com_crashlytics_export_strings.xml
68
+ crashlytics.properties
69
+ crashlytics-build.properties
70
+ fabric.properties
71
+
72
+ ### PyCharm+all Patch ###
73
+ # Ignores the whole .idea folder and all .iml files
74
+ # See https://github.com/joeblau/gitignore.io/issues/186 and https://github.com/joeblau/gitignore.io/issues/360
75
+
76
+ .idea/
77
+
78
+ # Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-249601023
79
+
80
+ *.iml
81
+ modules.xml
82
+ .idea/misc.xml
83
+ *.ipr
84
+
85
+ ### Python ###
86
+ # Byte-compiled / optimized / DLL files
87
+ __pycache__/
88
+ *.py[cod]
89
+ *$py.class
90
+
91
+ # C extensions
92
+ *.so
93
+
94
+ # Distribution / packaging
95
+ .Python
96
+ build/
97
+ develop-eggs/
98
+ dist/
99
+ downloads/
100
+ eggs/
101
+ .eggs/
102
+ lib/
103
+ lib64/
104
+ parts/
105
+ sdist/
106
+ var/
107
+ wheels/
108
+ *.egg-info/
109
+ .installed.cfg
110
+ *.egg
111
+
112
+ # PyInstaller
113
+ # Usually these files are written by a python script from a template
114
+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
115
+ *.manifest
116
+ *.spec
117
+
118
+ # Installer logs
119
+ pip-log.txt
120
+ pip-delete-this-directory.txt
121
+
122
+ # Unit test / coverage reports
123
+ htmlcov/
124
+ .tox/
125
+ .coverage
126
+ .coverage.*
127
+ .cache
128
+ .pytest_cache/
129
+ nosetests.xml
130
+ coverage.xml
131
+ *.cover
132
+ .hypothesis/
133
+
134
+ # Translations
135
+ *.mo
136
+ *.pot
137
+
138
+ # Flask stuff:
139
+ instance/
140
+ .webassets-cache
141
+
142
+ # Scrapy stuff:
143
+ .scrapy
144
+
145
+ # Sphinx documentation
146
+ docs/_build/
147
+
148
+ # PyBuilder
149
+ target/
150
+
151
+ # Jupyter Notebook
152
+ .ipynb_checkpoints
153
+
154
+ # pyenv
155
+ .python-version
156
+
157
+ # celery beat schedule file
158
+ celerybeat-schedule.*
159
+
160
+ # SageMath parsed files
161
+ *.sage.py
162
+
163
+ # Environments
164
+ .env
165
+ .venv
166
+ env/
167
+ venv/
168
+ ENV/
169
+ env.bak/
170
+ venv.bak/
171
+
172
+ # Spyder project settings
173
+ .spyderproject
174
+ .spyproject
175
+
176
+ # Rope project settings
177
+ .ropeproject
178
+
179
+ # mkdocs documentation
180
+ /site
181
+
182
+ # mypy
183
+ .mypy_cache/
184
+
185
+
186
+ # End of https://www.gitignore.io/api/linux,python,pycharm+all
pypte-1.0.0/CHANGELOG.md ADDED
@@ -0,0 +1,163 @@
1
+ # CHANGELOG
2
+
3
+
4
+
5
+ ## v0.2.0 (2024-04-21)
6
+
7
+ ### Chore
8
+
9
+ * chore: pipeline adjustments ([`2ca8d45`](https://github.com/patrk/pyPTE/commit/2ca8d4516d7730620fda0c526d32852092d5f5a5))
10
+
11
+ ### Feature
12
+
13
+ * feat: add new tests, type hinting, resolve issues (#17) ([`945ce2e`](https://github.com/patrk/pyPTE/commit/945ce2e7d3d11bde238965211d5d7f41a4f433cf))
14
+
15
+ ### Fix
16
+
17
+ * fix: (crucial) swapped dimensions in PTE calculation
18
+
19
+ * fix: (crucial) swapped dimensions in PTE calculation
20
+
21
+ * fix: predictions calculation using n_samples instead of m_channels ([`3ca8e9b`](https://github.com/patrk/pyPTE/commit/3ca8e9b0fa8e173a7b6bf31b0a78e45ef0e4a2ed))
22
+
23
+ * fix: (crucial) swapped dimensions in PTE calculation (#28) ([`eeb59fc`](https://github.com/patrk/pyPTE/commit/eeb59fc96d586aac389028f32687487bd754b964))
24
+
25
+ * fix: swapped axes of time series and phase array (#27) ([`e018213`](https://github.com/patrk/pyPTE/commit/e018213c473bc2ef873f7b4759b50e467c70c464))
26
+
27
+ * fix: get_phase swapped dimensions, get_phase wrongly expected the time_series of shape (n_samples, m_channels) instead of (m_channels, n_samples) (#26) ([`4bf6b5e`](https://github.com/patrk/pyPTE/commit/4bf6b5e83c48c12b302750d2095297b4772e8a56))
28
+
29
+ * fix: adjust zero-crossing detection: shift by 1, include all data points (#19) ([`4f9d2b4`](https://github.com/patrk/pyPTE/commit/4f9d2b4dbc26c843ea7a51c1c1e92921e60b74c4))
30
+
31
+ * fix: actions pipeline (#18) ([`aac8222`](https://github.com/patrk/pyPTE/commit/aac8222868b7b46573e338d366cdda66ecb63ec2))
32
+
33
+ ### Unknown
34
+
35
+ * Bump idna from 3.6 to 3.7 (#24) ([`37932db`](https://github.com/patrk/pyPTE/commit/37932db209488852d5b35a42c096bed5ec3e6519))
36
+
37
+ * Patrk patch 1 (#23)
38
+
39
+ * Update README.md ([`26dfddc`](https://github.com/patrk/pyPTE/commit/26dfddc85a6c4dea5f5076f48dc02ac01f6aa356))
40
+
41
+
42
+ ## v0.1.0 (2024-04-03)
43
+
44
+ ### Unknown
45
+
46
+ * Merge pull request #16 from patrk/dependabot/pip/scipy-1.11.1 ([`fcac46c`](https://github.com/patrk/pyPTE/commit/fcac46c7ad0798401c4379b048a5e3c400c2a5ca))
47
+
48
+ * Bump scipy from 1.7.1 to 1.11.1
49
+
50
+ Bumps [scipy](https://github.com/scipy/scipy) from 1.7.1 to 1.11.1.
51
+ - [Release notes](https://github.com/scipy/scipy/releases)
52
+ - [Commits](https://github.com/scipy/scipy/compare/v1.7.1...v1.11.1)
53
+
54
+ ---
55
+ updated-dependencies:
56
+ - dependency-name: scipy
57
+ dependency-type: direct:production
58
+ ...
59
+
60
+ Signed-off-by: dependabot[bot] <support@github.com> ([`7e7f5e8`](https://github.com/patrk/pyPTE/commit/7e7f5e816cf750bcd674b751deea9d0e673f2d5e))
61
+
62
+ * Merge pull request #15 from patrk/14-the-definition-of-bin-width
63
+
64
+ Use number of samples in bin size calculation ([`15d3ada`](https://github.com/patrk/pyPTE/commit/15d3ada585e0bc3c246b9bb4aee7a698d0504cbc))
65
+
66
+ * Use number of samples in bin size calculation ([`45c52a5`](https://github.com/patrk/pyPTE/commit/45c52a5b2a75584fb714f96afadd563517728e47))
67
+
68
+ * Merge pull request #13 from patrk/patrk-patch-1
69
+
70
+ Update README.md ([`7e3ddc0`](https://github.com/patrk/pyPTE/commit/7e3ddc0f6c520b51fd3873b5ac34d9caa7110bf6))
71
+
72
+ * Update README.md ([`6091605`](https://github.com/patrk/pyPTE/commit/60916054c5c8ebddfa7e6f8fcdf8a062fc4c4224))
73
+
74
+ * refined README.md equations ([`0d59bc0`](https://github.com/patrk/pyPTE/commit/0d59bc08824ff4a07e09440be25761cf94d6e1f3))
75
+
76
+ * refined README.md equations ([`dcdfbf2`](https://github.com/patrk/pyPTE/commit/dcdfbf2d9b9e30e4725b59a516f04689aa906726))
77
+
78
+ * refined README.md
79
+ specified versions in requirements.txt ([`bd644f3`](https://github.com/patrk/pyPTE/commit/bd644f32b07d8304bce171f97e456f1c171231c9))
80
+
81
+ * refined README.md ([`feb11db`](https://github.com/patrk/pyPTE/commit/feb11dbdf37ca47ad96c003a09bbe32492035491))
82
+
83
+ * Merge pull request #10 from Ku4eruk/master
84
+
85
+ compute_PTE matrix dimension changed ([`152a5bb`](https://github.com/patrk/pyPTE/commit/152a5bbcddf2cc47f2b01e78bcd5d2b485681d94))
86
+
87
+ * compute_PTE matrix dimension changed ([`5b1c3a8`](https://github.com/patrk/pyPTE/commit/5b1c3a8cdf0d1321cd10417934a355b6d6b09dfb))
88
+
89
+ * api-doc ([`2e165d9`](https://github.com/patrk/pyPTE/commit/2e165d9d9bebfa1c01477190e762177ba3956f10))
90
+
91
+ * api-doc ([`70f240a`](https://github.com/patrk/pyPTE/commit/70f240ac644d655a4f25db2702c24e92bec97d39))
92
+
93
+ * apidoc ([`edf9ff8`](https://github.com/patrk/pyPTE/commit/edf9ff84ad1a239073206540d35f2507f52d7e16))
94
+
95
+ * mne_tools doc ([`4fee056`](https://github.com/patrk/pyPTE/commit/4fee05657efa5a610b22a6582dc476a8cb9e727d))
96
+
97
+ * mne_tools doc ([`d49cbb4`](https://github.com/patrk/pyPTE/commit/d49cbb4e1bfaa6c47ab036e68fa31ff63fdfeeab))
98
+
99
+ * mne_tools doc ([`cdc5c60`](https://github.com/patrk/pyPTE/commit/cdc5c608f24e8e5cd4b26e2a8a9a4dc3e008230d))
100
+
101
+ * Merge remote-tracking branch 'origin/master' ([`1d45cbf`](https://github.com/patrk/pyPTE/commit/1d45cbfa271613bd834097331cff2056e2631482))
102
+
103
+ * mne_tools doc ([`30f9a7b`](https://github.com/patrk/pyPTE/commit/30f9a7b3024193d5acf80eb122a598f7580636a4))
104
+
105
+ * Update README.rst ([`372e9d3`](https://github.com/patrk/pyPTE/commit/372e9d3d66be2db6886ccffeff8b83a47127fd14))
106
+
107
+ * mne_tools doc ([`2ec652c`](https://github.com/patrk/pyPTE/commit/2ec652c97758e21f760d4c4d9475e85193228dc2))
108
+
109
+ * mne_tools doc ([`39fd656`](https://github.com/patrk/pyPTE/commit/39fd6561be88bccc5cfae58b1f607d76f1200e94))
110
+
111
+ * clean up neural mass model ([`db1f5b5`](https://github.com/patrk/pyPTE/commit/db1f5b5a6b56276a164787d03e60690d74f7803b))
112
+
113
+ * fixed bug in multiprocessing ([`f99a6aa`](https://github.com/patrk/pyPTE/commit/f99a6aa8b4cb210d3e3b2e38fae492575f479678))
114
+
115
+ * bug in stats fixed ([`2dcf3da`](https://github.com/patrk/pyPTE/commit/2dcf3da406a440460006cb8c021b0a74bbcab419))
116
+
117
+ * Merge branch 'master' of https://github.com/patrk/pyPTE ([`9558d5a`](https://github.com/patrk/pyPTE/commit/9558d5ad689658d19d62070afba62dcd884ec5f5))
118
+
119
+ * docs ([`cb3f783`](https://github.com/patrk/pyPTE/commit/cb3f78328e86bdc061301ec69a3225c586ed9c23))
120
+
121
+ * docs ([`c619210`](https://github.com/patrk/pyPTE/commit/c619210c4f5dcae9cd15aaec845ca841c060e646))
122
+
123
+ * Update requirements.txt ([`15b3121`](https://github.com/patrk/pyPTE/commit/15b3121869bcc33ffef22a80ae5c40f1bee56d62))
124
+
125
+ * Create requirements.txt ([`69cba9c`](https://github.com/patrk/pyPTE/commit/69cba9c52a5e7d9625dd87ab5488338f790b0658))
126
+
127
+ * docs ([`41d8e65`](https://github.com/patrk/pyPTE/commit/41d8e6530de70f350933451186d4b966ce1f4534))
128
+
129
+ * Create README.rst ([`a625a11`](https://github.com/patrk/pyPTE/commit/a625a11fd42f5b8c547fcf90e27f525c8ba15faf))
130
+
131
+ * refactor ([`ae52140`](https://github.com/patrk/pyPTE/commit/ae52140c9176527f513e37594c0c7c7aa58645ce))
132
+
133
+ * wilcoxon test on PTE ([`b2ee93e`](https://github.com/patrk/pyPTE/commit/b2ee93e2f1e8b435b5b98126bb5d0a8564560190))
134
+
135
+ * interpolate missing mne channels ([`a984e94`](https://github.com/patrk/pyPTE/commit/a984e9423a95aece91b557d82b7f2bfb4715a026))
136
+
137
+ * test ([`b438815`](https://github.com/patrk/pyPTE/commit/b438815018e69af5ad59a2d2d7d2e6b61a788518))
138
+
139
+ * cleaning up ([`dc5df57`](https://github.com/patrk/pyPTE/commit/dc5df57cd05ab2584c3d5926bbfa68cfc684a2c3))
140
+
141
+ * docs ([`11181a5`](https://github.com/patrk/pyPTE/commit/11181a51377b94517ff87ce39b668c15e865049c))
142
+
143
+ * cleaning up ([`fa3da91`](https://github.com/patrk/pyPTE/commit/fa3da919b71d213da49190b78530028199eb2502))
144
+
145
+ * docs ([`a9507be`](https://github.com/patrk/pyPTE/commit/a9507be19e780fdb73a8dc600ac84d52e7d873f5))
146
+
147
+ * docs ([`5620ab6`](https://github.com/patrk/pyPTE/commit/5620ab6211b518f58a8c4eb893b5ce88b95b6d23))
148
+
149
+ * docs ([`0537be8`](https://github.com/patrk/pyPTE/commit/0537be8759642885d080b2d0f18ad5fce8b212cb))
150
+
151
+ * project restructuring ([`7e18306`](https://github.com/patrk/pyPTE/commit/7e18306b27ab847c18f45a177c59659cf7d8e3c1))
152
+
153
+ * cleaning up ([`27bfd60`](https://github.com/patrk/pyPTE/commit/27bfd601404e7f56613f6f692459b042d0503ef0))
154
+
155
+ * cleaning up ([`41d3d2e`](https://github.com/patrk/pyPTE/commit/41d3d2e9dd9040d1bc75fe8c0e16b0f46e3a1b03))
156
+
157
+ * cleaning up ([`5c1f890`](https://github.com/patrk/pyPTE/commit/5c1f890881232c2b54382d185333b4e690af2136))
158
+
159
+ * initial commit ([`bbb069e`](https://github.com/patrk/pyPTE/commit/bbb069e0f32fe9f28da9bef9aa7471dbe3003cde))
160
+
161
+ * .gitignore ([`6a286c6`](https://github.com/patrk/pyPTE/commit/6a286c62f75e9436ec6438841c455c7917e97cba))
162
+
163
+ * Initial commit ([`139fed5`](https://github.com/patrk/pyPTE/commit/139fed58b71652c549b0e39a4d9d06bd3ec02cd5))