Codebase list libsbml / 1397ff4
Enforce Python3 interpreter in examples Andreas Tille 4 years ago
3 changed file(s) with 514 addition(s) and 0 deletion(s). Raw diff Collapse all Expand all
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debian/changelog less more
88 Closes: #949195
99 * Fix installation path of Python modules
1010 Closes: #922486
11 * Enforce Python3 interpreter in examples
1112
1213 -- Andreas Tille <tille@debian.org> Sun, 26 Jan 2020 20:54:35 +0100
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debian/patches/fix_python_interpreter.patch less more
0 Author: Andreas Tille <tille@debian.org>
1 Last-Update: Sun, 26 Jan 2020 20:54:35 +0100
2 Descriptions: Examples are calling Python2 which is not helpful. This patch enforces Python3
3 Note: One upstream file contains a space in file name:
4 examples/python/distrib/createStatisticsExample .py
5 Quilt seems unable to deal with this - if users want to use this
6 example they simply need to fix it manually.
7
8 --- a/docs/src/filters/doc-filter-c.py
9 +++ b/docs/src/filters/doc-filter-c.py
10 @@ -1,4 +1,4 @@
11 -#!/usr/bin/env python
12 +#!/usr/bin/python3
13 #
14 # @file doc-filter-c.py
15 # @brief Post-process libSBML's source files for creating C docs with Doxygen.
16 --- a/docs/src/filters/doc-filter-csharp.py
17 +++ b/docs/src/filters/doc-filter-csharp.py
18 @@ -1,4 +1,4 @@
19 -#!/usr/bin/env python
20 +#!/usr/bin/python3
21 #
22 # @file doc-filter-csharp.py
23 # @brief Post-process libSBML's csharp doc strings for use by Doxygen.
24 --- a/docs/src/filters/doc-filter-python.py
25 +++ b/docs/src/filters/doc-filter-python.py
26 @@ -1,4 +1,4 @@
27 -#!/usr/bin/env python
28 +#!/usr/bin/python3
29 # -*- python-indent-offset: 2 -*-
30 #
31 # @file doc-filter-python.py
32 --- a/docs/src/utilities/compare-classes.py
33 +++ b/docs/src/utilities/compare-classes.py
34 @@ -1,4 +1,4 @@
35 -#!/usr/bin/env python
36 +#!/usr/bin/python3
37 #
38 # @file compare-classes.py
39 # @brief Compare classes in C++ code to those documented via Doxygen
40 --- a/docs/src/utilities/compare-constants.py
41 +++ b/docs/src/utilities/compare-constants.py
42 @@ -1,4 +1,4 @@
43 -#!/usr/bin/env python
44 +#!/usr/bin/python3
45 #
46 # @file compare-constants.py
47 # @brief Compare the constants in the substitution files to the current list
48 --- a/docs/src/utilities/generate-class-name-list.py
49 +++ b/docs/src/utilities/generate-class-name-list.py
50 @@ -1,4 +1,4 @@
51 -#!/usr/bin/env python
52 +#!/usr/bin/python3
53 #
54 # @file generate-class-name-list.py
55 # @brief Generate a list of class & enum names defined in libSBML
56 --- a/docs/src/utilities/generate-converters-list.py
57 +++ b/docs/src/utilities/generate-converters-list.py
58 @@ -1,4 +1,4 @@
59 -#!/usr/bin/env python
60 +#!/usr/bin/python3
61 #
62 # @file generate-converters-list.py
63 # @brief Generate libsbml-converters.txt, a list of SBML converter classes
64 --- a/docs/src/utilities/generate-cplusplus-class-names.py
65 +++ b/docs/src/utilities/generate-cplusplus-class-names.py
66 @@ -1,4 +1,4 @@
67 -#!/usr/bin/env python
68 +#!/usr/bin/python3
69 #
70 # @file generate-cplusplus-class-names.py
71 # @brief Generate a list of classes defined in libSBML
72 --- a/docs/src/utilities/generate-extensions-summary.py
73 +++ b/docs/src/utilities/generate-extensions-summary.py
74 @@ -1,4 +1,4 @@
75 -#!/usr/bin/env python
76 +#!/usr/bin/python3
77 #
78 # @file generate-extensions-summary.py
79 # @brief Create a page summarizing libSBML L3 extensions for Java
80 --- a/docs/src/utilities/generate-pkg-stylesheet.py
81 +++ b/docs/src/utilities/generate-pkg-stylesheet.py
82 @@ -1,4 +1,4 @@
83 -#!/usr/bin/env python
84 +#!/usr/bin/python3
85 #
86 # @file generate-pkg-stylesheet.py
87 # @brief Create a stylesheet for libSBML package extensions
88 --- a/docs/src/utilities/pythondocpreprocessor.py
89 +++ b/docs/src/utilities/pythondocpreprocessor.py
90 @@ -1,4 +1,4 @@
91 -#!/usr/bin/env python
92 +#!/usr/bin/python3
93
94 import re
95 import sys
96 --- a/examples/python/addCVTerms.py
97 +++ b/examples/python/addCVTerms.py
98 @@ -1,4 +1,4 @@
99 -#!/usr/bin/env python
100 +#!/usr/bin/python3
101 ##
102 ## \file addCVTerms.py
103 ## \brief adds controlled vocabulary terms to a species in a model
104 --- a/examples/python/addCustomValidator.py
105 +++ b/examples/python/addCustomValidator.py
106 @@ -1,4 +1,4 @@
107 -#!/usr/bin/env python
108 +#!/usr/bin/python3
109 ##
110 ## @file addCustomValidator.py
111 ## @brief Example creating a custom validator to be called during validation
112 --- a/examples/python/addModelHistory.py
113 +++ b/examples/python/addModelHistory.py
114 @@ -1,4 +1,4 @@
115 -#!/usr/bin/env python
116 +#!/usr/bin/python3
117 ##
118 ## \file addModelHistory.py
119 ## \brief adds Model History to a model
120 --- a/examples/python/addingEvidenceCodes_1.py
121 +++ b/examples/python/addingEvidenceCodes_1.py
122 @@ -1,4 +1,4 @@
123 -#!/usr/bin/env python
124 +#!/usr/bin/python3
125 ##
126 ## \file addingEvidenceCodes_1.py
127 ## \brief adds controlled vocabulary terms to a reaction in a model
128 --- a/examples/python/addingEvidenceCodes_2.py
129 +++ b/examples/python/addingEvidenceCodes_2.py
130 @@ -1,4 +1,4 @@
131 -#!/usr/bin/env python
132 +#!/usr/bin/python3
133 ##
134 ## \file addingEvidenceCodes_2.py
135 ## \brief adds evidence codes to a species in a model
136 --- a/examples/python/appendAnnotation.py
137 +++ b/examples/python/appendAnnotation.py
138 @@ -1,4 +1,4 @@
139 -#!/usr/bin/env python
140 +#!/usr/bin/python3
141 ##
142 ## \file appendAnnotation.py
143 ## \brief adds annotation strings to a model and a species
144 --- a/examples/python/append_to_note.py
145 +++ b/examples/python/append_to_note.py
146 @@ -1,4 +1,4 @@
147 -#!/usr/bin/env python
148 +#!/usr/bin/python3
149 ##
150 ## \file append_to_note.py
151 ## \brief adds to the notes of an element in a document
152 --- a/examples/python/arrays/flattenArrays.py
153 +++ b/examples/python/arrays/flattenArrays.py
154 @@ -1,4 +1,4 @@
155 -#!/usr/bin/env python
156 +#!/usr/bin/python3
157 ##
158 ## @file flattenArrays.py
159 ## @brief Flattens the arrays code from the given SBML file.
160 --- a/examples/python/callExternalValidator.py
161 +++ b/examples/python/callExternalValidator.py
162 @@ -1,4 +1,4 @@
163 -#!/usr/bin/env python
164 +#!/usr/bin/python3
165 ##
166 ## @file callExternalValidator.py
167 ## @brief Example that shows how to call an external program for validation
168 --- a/examples/python/comp/flattenModel.py
169 +++ b/examples/python/comp/flattenModel.py
170 @@ -1,4 +1,4 @@
171 -#!/usr/bin/env python
172 +#!/usr/bin/python3
173 ##
174 ## @file flattenModel.py
175 ## @brief Flattens the comp code from the given SBML file.
176 --- a/examples/python/convertSBML.py
177 +++ b/examples/python/convertSBML.py
178 @@ -1,4 +1,4 @@
179 -#!/usr/bin/env python
180 +#!/usr/bin/python3
181 ##
182 ## @file convertSBML.py
183 ## @brief Converts SBML documents between levels
184 --- a/examples/python/createExampleSBML.py
185 +++ b/examples/python/createExampleSBML.py
186 @@ -1,4 +1,4 @@
187 -#!/usr/bin/env python
188 +#!/usr/bin/python3
189 ##
190 ## @file createExampleSBML.py
191 ## @brief Creates example SBML models presented in the SBML specification.
192 --- a/examples/python/createSimpleModel.py
193 +++ b/examples/python/createSimpleModel.py
194 @@ -1,4 +1,4 @@
195 -#!/usr/bin/env python
196 +#!/usr/bin/python3
197 ##
198 ## @file createSampleModel.py
199 ## @brief Creates a simple SBML model and prints it to stdout.
200 --- a/examples/python/distrib/createNormalExample.py
201 +++ b/examples/python/distrib/createNormalExample.py
202 @@ -1,4 +1,4 @@
203 -#!/usr/bin/env python
204 +#!/usr/bin/python3
205 # @file createNormalExample.py
206 # @brief SBML distrib example
207 # @author Sarah Keating
208 --- a/examples/python/echoSBML.py
209 +++ b/examples/python/echoSBML.py
210 @@ -1,4 +1,4 @@
211 -#!/usr/bin/env python
212 +#!/usr/bin/python3
213 ##
214 ## @file echoSBML.py
215 ## @brief Echos an SBML model.
216 --- a/examples/python/evaluateCustomMath.py
217 +++ b/examples/python/evaluateCustomMath.py
218 @@ -1,4 +1,4 @@
219 -#!/usr/bin/env python
220 +#!/usr/bin/python3
221 ##
222 ## @file evaluateCustomMath.py
223 ## @brief evaluates the given formula
224 --- a/examples/python/fbc/convertCobraToFbc.py
225 +++ b/examples/python/fbc/convertCobraToFbc.py
226 @@ -1,4 +1,4 @@
227 -#!/usr/bin/env python
228 +#!/usr/bin/python3
229 ##
230 ## @file convertCobraToFbc.py
231 ## @brief Convert COBRA L2 to L3 with FBC
232 --- a/examples/python/fbc/convertFbcToCobra.py
233 +++ b/examples/python/fbc/convertFbcToCobra.py
234 @@ -1,4 +1,4 @@
235 -#!/usr/bin/env python
236 +#!/usr/bin/python3
237 ##
238 ## @file convertFbcToCobra.py
239 ## @brief Convert L3 with FBC to COBRA L2
240 --- a/examples/python/fbc/fbc_example1.py
241 +++ b/examples/python/fbc/fbc_example1.py
242 @@ -1,4 +1,4 @@
243 -#!/usr/bin/env python
244 +#!/usr/bin/python3
245 #
246 # @file fbc_example1.py
247 # @brief SBML FBC example
248 --- a/examples/python/getAllElementsWithNotes.py
249 +++ b/examples/python/getAllElementsWithNotes.py
250 @@ -1,4 +1,4 @@
251 -#!/usr/bin/env python
252 +#!/usr/bin/python3
253 ##
254 ## @file getAllElementsWithNotes.py
255 ## @brief Utility program, demonstrating how to use the element filter
256 --- a/examples/python/groups/groups_example1.py
257 +++ b/examples/python/groups/groups_example1.py
258 @@ -1,4 +1,4 @@
259 -#!/usr/bin/env python
260 +#!/usr/bin/python3
261 #
262 # @file groups_example1.py
263 # @brief SBML Groups example
264 --- a/examples/python/groups/print_groups.py
265 +++ b/examples/python/groups/print_groups.py
266 @@ -1,4 +1,4 @@
267 -#!/usr/bin/env python
268 +#!/usr/bin/python3
269 ##
270 ## @file print_groups.py
271 ## @brief Example printing the groups contained in an sbml file
272 --- a/examples/python/inlineFunctionDefinitions.py
273 +++ b/examples/python/inlineFunctionDefinitions.py
274 @@ -1,4 +1,4 @@
275 -#!/usr/bin/env python
276 +#!/usr/bin/python3
277 ##
278 ## @file inlineFunctionDefinitions.py
279 ## @brief expands function definitions where used
280 --- a/examples/python/inlineInitialAssignments.py
281 +++ b/examples/python/inlineInitialAssignments.py
282 @@ -1,4 +1,4 @@
283 -#!/usr/bin/env python
284 +#!/usr/bin/python3
285 ##
286 ## @file inlineInitialAssignments.py
287 ## @brief inlines all initial assignments directly
288 --- a/examples/python/layout/convertLayout.py
289 +++ b/examples/python/layout/convertLayout.py
290 @@ -1,4 +1,4 @@
291 -#!/usr/bin/env python
292 +#!/usr/bin/python3
293 ##
294 ## @file convertLayout.py
295 ## @author Frank T. Bergmann
296 --- a/examples/python/layout/example1-L3.py
297 +++ b/examples/python/layout/example1-L3.py
298 @@ -1,4 +1,4 @@
299 -#!/usr/bin/env python
300 +#!/usr/bin/python3
301
302 #
303 # \file example1-L3.py
304 --- a/examples/python/layout/example1.py
305 +++ b/examples/python/layout/example1.py
306 @@ -1,4 +1,4 @@
307 -#!/usr/bin/env python
308 +#!/usr/bin/python3
309
310 #
311 # \file example1.py
312 --- a/examples/python/printAnnotation.py
313 +++ b/examples/python/printAnnotation.py
314 @@ -1,4 +1,4 @@
315 -#!/usr/bin/env python
316 +#!/usr/bin/python3
317 ##
318 ## @file printAnnotation.py
319 ## @brief Prints annotation strings for each element
320 --- a/examples/python/printMath.py
321 +++ b/examples/python/printMath.py
322 @@ -1,4 +1,4 @@
323 -#!/usr/bin/env python
324 +#!/usr/bin/python3
325 ##
326 ## @file printMath.py
327 ## @brief Prints Rule, Reaction, and Event formulas in a given SBML Document
328 --- a/examples/python/printNotes.py
329 +++ b/examples/python/printNotes.py
330 @@ -1,4 +1,4 @@
331 -#!/usr/bin/env python
332 +#!/usr/bin/python3
333 ##
334 ## @file printNotes.py
335 ## @brief Prints notes strings for each element
336 --- a/examples/python/printRegisteredPackages.py
337 +++ b/examples/python/printRegisteredPackages.py
338 @@ -1,4 +1,4 @@
339 -#!/usr/bin/env python
340 +#!/usr/bin/python3
341 ##
342 ## @file printRegisteredPackages.py
343 ## @brief Prints the registered packages for this libSBML
344 --- a/examples/python/printSBML.py
345 +++ b/examples/python/printSBML.py
346 @@ -1,4 +1,4 @@
347 -#!/usr/bin/env python
348 +#!/usr/bin/python3
349 ##
350 ## @file printModel.py
351 ## @brief Prints some information about the top-level model
352 --- a/examples/python/printUnits.py
353 +++ b/examples/python/printUnits.py
354 @@ -1,4 +1,4 @@
355 -#!/usr/bin/env python
356 +#!/usr/bin/python3
357 ##
358 ## @file printUnits.py
359 ## @brief Prints some unit information about the model
360 --- a/examples/python/printsupported.py
361 +++ b/examples/python/printsupported.py
362 @@ -1,4 +1,4 @@
363 -#!/usr/bin/env python
364 +#!/usr/bin/python3
365 ##
366 ## @file printsupported.cs
367 ## @brief Prints all SBML Levels and Versions supported by this version
368 --- a/examples/python/promoteParameters.py
369 +++ b/examples/python/promoteParameters.py
370 @@ -1,4 +1,4 @@
371 -#!/usr/bin/env python
372 +#!/usr/bin/python3
373 ##
374 ## @file promoteParameters.py
375 ## @brief promotes all local to global parameters
376 --- a/examples/python/qual/qual_example1.py
377 +++ b/examples/python/qual/qual_example1.py
378 @@ -1,4 +1,4 @@
379 -#!/usr/bin/env python
380 +#!/usr/bin/python3
381 ##
382 ## @file qual_example1.py
383 ## @brief Qual Example
384 --- a/examples/python/readSBML.py
385 +++ b/examples/python/readSBML.py
386 @@ -1,4 +1,4 @@
387 -#!/usr/bin/env python
388 +#!/usr/bin/python3
389 ##
390 ## @file readSBML.py
391 ## @brief Similar to validateSBML, but without the validation
392 --- a/examples/python/replaceOneFD.py
393 +++ b/examples/python/replaceOneFD.py
394 @@ -1,4 +1,4 @@
395 -#!/usr/bin/env python
396 +#!/usr/bin/python3
397 ##
398 ## @file replaceOneFD.py
399 ## @brief replaces a given function definition in a specific part of the model
400 --- a/examples/python/setIdFromNames.py
401 +++ b/examples/python/setIdFromNames.py
402 @@ -1,4 +1,4 @@
403 -#!/usr/bin/env python
404 +#!/usr/bin/python3
405 ##
406 ## @file setIdFromNames.py
407 ## @brief Utility program, renaming all SIds that also has
408 --- a/examples/python/stringInput.py
409 +++ b/examples/python/stringInput.py
410 @@ -1,4 +1,4 @@
411 -#!/usr/bin/env python
412 +#!/usr/bin/python3
413 ##
414 ## @file stringInput.py
415 ## @brief illustrates how libSBML deals with string and unicode input
416 --- a/examples/python/stripPackage.py
417 +++ b/examples/python/stripPackage.py
418 @@ -1,4 +1,4 @@
419 -#!/usr/bin/env python
420 +#!/usr/bin/python3
421 ##
422 ## @file stripPackage.py
423 ## @brief Strips the given package from the given SBML file.
424 --- a/examples/python/translateMath.py
425 +++ b/examples/python/translateMath.py
426 @@ -1,4 +1,4 @@
427 -#!/usr/bin/env python
428 +#!/usr/bin/python3
429 ##
430 ## @file translateMath.py
431 ## @brief Translates infix formulas into MathML and vice-versa
432 --- a/examples/python/unsetAnnotation.py
433 +++ b/examples/python/unsetAnnotation.py
434 @@ -1,4 +1,4 @@
435 -#!/usr/bin/env python
436 +#!/usr/bin/python3
437 ##
438 ## @file unsetAnnotation.py
439 ## @brief unset annotation for each element
440 --- a/examples/python/unsetNotes.py
441 +++ b/examples/python/unsetNotes.py
442 @@ -1,4 +1,4 @@
443 -#!/usr/bin/env python
444 +#!/usr/bin/python3
445 ##
446 ## @file unsetNotes.py
447 ## @brief unset notes for each element
448 --- a/examples/python/validateSBML.py
449 +++ b/examples/python/validateSBML.py
450 @@ -1,4 +1,4 @@
451 -#!/usr/bin/env python
452 +#!/usr/bin/python3
453 ##
454 ## @file validateSBML.py
455 ## @brief Validates one or more SBML files
456 --- a/examples/python/validateSBMLWithCallback.py
457 +++ b/examples/python/validateSBMLWithCallback.py
458 @@ -1,4 +1,4 @@
459 -#!/usr/bin/env python
460 +#!/usr/bin/python3
461 ##
462 ## @file validateSBML.py
463 ## @brief Validates one or more SBML files
464 --- a/src/bindings/python/doc-converter/prettytable.py
465 +++ b/src/bindings/python/doc-converter/prettytable.py
466 @@ -1,4 +1,4 @@
467 -#!/usr/bin/env python
468 +#!/usr/bin/python3
469 #
470 # Copyright (c) 2009-2013, Luke Maurits <luke@maurits.id.au>
471 # All rights reserved.
472 --- a/src/bindings/python/doc-converter/rewrite_pydoc.py
473 +++ b/src/bindings/python/doc-converter/rewrite_pydoc.py
474 @@ -1,4 +1,4 @@
475 -#!/usr/bin/env python
476 +#!/usr/bin/python3
477 ##
478 ## @file rewrite_pydoc.py
479 ## @brief Convert libSBML Python doc file to something readable as docstrings
480 --- a/src/bindings/python/test.py
481 +++ b/src/bindings/python/test.py
482 @@ -1,4 +1,4 @@
483 -#!/usr/bin/env python
484 +#!/usr/bin/python3
485 ##
486 ## @file test.py
487 ## @brief AutoRunner for Python test scripts
488 --- a/src/bindings/swig/libsbmlutils.py
489 +++ b/src/bindings/swig/libsbmlutils.py
490 @@ -1,4 +1,4 @@
491 -#!/usr/bin/env python
492 +#!/usr/bin/python3
493 #
494 # @file libsbmlutils.py
495 # @brief Common utility code used by some of our other Python programs.
496 --- a/src/bindings/swig/swigdoc.py
497 +++ b/src/bindings/swig/swigdoc.py
498 @@ -1,4 +1,4 @@
499 -#!/usr/bin/env python
500 +#!/usr/bin/python3
501 #
502 # @file swigdoc.py
503 # @brief Creates documentation for C#, Java, Python, and Perl.
504 --- a/examples/python/fbc/print_gene_product_association.py
505 +++ b/examples/python/fbc/print_gene_product_association.py
506 @@ -1,4 +1,4 @@
507 -#!/bin/env python
508 +#!/usr/bin/python3
509 import libsbml
510 import sys
511
+1
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debian/patches/series less more
99 remove_SBMLDoclet.patch
1010 fix_cmake_configuration.patch
1111 fix_build_issue.patch
12 fix_python_interpreter.patch