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Implement automatic tool generation based on the source code of the tool #1263

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merged 72 commits into from
Sep 14, 2023
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386ce5e
added CLI arg
Kulivox Aug 8, 2022
935dc75
migrated code from pygalgen
Kulivox Aug 8, 2022
d611544
proof of concept integration of parser extraction
Kulivox Aug 8, 2022
e13262b
implemented input section automatic generation prototype
Kulivox Aug 20, 2022
1a5afb4
applied formatting rules
Kulivox Aug 20, 2022
7eb9b35
created new template macro for autogenerated content
Kulivox Aug 21, 2022
9119034
moved source file
Kulivox Aug 21, 2022
3b09043
introduced fixes to bugs caused by migration
Kulivox Aug 21, 2022
1170866
reverted makefile change
Kulivox Aug 22, 2022
e703fcc
reverted accidental delete
Kulivox Aug 22, 2022
f9fd718
removed unused class
Kulivox Aug 22, 2022
00c0dc9
added subparser compatibility
Kulivox Sep 18, 2022
49bf116
fix: refactoring
Kulivox Sep 18, 2022
4eb4e1e
feat: full subparsers support all imports needed
Kulivox Sep 18, 2022
3a85106
revert: unknown imports removed
Kulivox Sep 18, 2022
14bfedd
feat: added tests, fixed mistakes
Kulivox Sep 24, 2022
9b96cbd
fix: lint
Kulivox Sep 24, 2022
12dc59c
feat: added unit tests for parser discovery and init
Kulivox Sep 25, 2022
d5759fa
feat: updated docs
Kulivox Sep 30, 2022
29bef45
fix: updated tests
Kulivox Sep 30, 2022
f18588c
fix: removed formatting from test data
Kulivox Sep 30, 2022
b32a0c2
fix: test data path
Kulivox Oct 1, 2022
564c9b8
fix: tests
Kulivox Oct 1, 2022
ee9a9f7
feat: conditionals, versions, and more
Kulivox Oct 1, 2022
9fc0e01
feat: max repeat
Kulivox Oct 1, 2022
e062f00
feat: output formatting
Kulivox Oct 2, 2022
47f207e
fix: input test data
Kulivox Oct 2, 2022
19bbcfb
feat: improved command gen
Kulivox Oct 2, 2022
569e50e
fix: regenerated test data
Kulivox Oct 2, 2022
2877b99
revert: accidental change
Kulivox Oct 2, 2022
b7b8695
fix: positional arguments are by default required, flags are optional
Kulivox Oct 11, 2022
ee3fd0a
feat: argument parser action tests
Kulivox Oct 11, 2022
de625ad
fix: incorrect command variable nesting
Kulivox Oct 11, 2022
1297e1f
fix: flake8 errors
Kulivox Feb 19, 2023
41a1383
fix: mypy and unit tests
Kulivox Feb 19, 2023
a613f16
feat(xml): xml is now being generated using lxml, instead of custom i…
Kulivox Feb 25, 2023
e330859
Drop call to ``escape_non_unicode_symbols``
nsoranzo Mar 1, 2023
4888b01
include autogen modules in packages
bernt-matthias Mar 4, 2023
5e43072
check for version command before using it
bernt-matthias Mar 4, 2023
cde911e
fix: unified section name transformation to a single function
Kulivox Mar 5, 2023
759bf61
fix: updated default indent of the command and removed formatting com…
Kulivox Mar 5, 2023
71d8118
fix: added quotes around text and data command parameters + test data
Kulivox Mar 5, 2023
1dd77ab
fix: added test cases for default choices + renamed constant
Kulivox Mar 5, 2023
b0bbf92
feat: added support for default values + regenerated test data and re…
Kulivox Mar 5, 2023
02090eb
feat: added automatic help generation
Kulivox Mar 5, 2023
59c5007
style: formatted using black
Kulivox Mar 20, 2023
5665807
fix(ParamDataType): removed redundant commas that converted enum valu…
Kulivox Mar 20, 2023
df5f40d
fix(xml_utils.param): added string conversion of default values to fi…
Kulivox Mar 20, 2023
241c0e4
style: lint
Kulivox Apr 23, 2023
34a1ea4
style: mypy
Kulivox Apr 23, 2023
3b7b673
fix(tool_builder): broken template
Kulivox Apr 23, 2023
77c9580
tests(test_autopygen_parser_discovery): updated test to pass on older…
Kulivox Apr 23, 2023
f2233c3
tests(test_add_argument_actions_autopygen): added ignore annotation t…
Kulivox Apr 23, 2023
ccef1ce
Merge branch 'master' into auto-tool-gen
Kulivox Apr 23, 2023
46cdfe0
allow for non-string options
bernt-matthias Jun 5, 2023
9d81118
fix argument type
bernt-matthias Jun 5, 2023
f52ad59
fix test and linting
bernt-matthias Aug 27, 2023
60e59f6
fix import order
bernt-matthias Aug 27, 2023
b0c83dc
get stdlib module names
bernt-matthias Aug 27, 2023
95d3426
stdlib_module_names needs to be hardcoded for py<3.10
bernt-matthias Aug 28, 2023
1f9b3cf
add missing import
bernt-matthias Aug 28, 2023
40311e9
import ordering
bernt-matthias Aug 28, 2023
dfb4545
more import sorting
bernt-matthias Aug 28, 2023
e0d718f
fix type comparisons
bernt-matthias Aug 28, 2023
ffbd9f6
alternative to stdlib modules list
bernt-matthias Aug 28, 2023
142239f
yet another try
bernt-matthias Aug 28, 2023
3f06801
one more try
bernt-matthias Aug 28, 2023
0cf009a
more
bernt-matthias Aug 29, 2023
ced1e98
one more try
bernt-matthias Aug 29, 2023
e2b6e2e
amend
bernt-matthias Aug 29, 2023
6cb3919
ignore typing error
bernt-matthias Aug 31, 2023
4cb7536
start (rudimentary) docs
bernt-matthias Sep 1, 2023
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4 changes: 4 additions & 0 deletions docs/commands/tool_init.rst
Original file line number Diff line number Diff line change
Expand Up @@ -51,5 +51,9 @@ Generate tool outline from given arguments.
'[email protected]').
--container TEXT Add a Docker image identifier for this tool.
--cwl Build a CWL tool instead of a Galaxy tool.
--autopygen TEXT Option for automatic generation of tool file, from
python source code that uses argparse. Parameter is
a path to source file containing definition of the
parser
--help Show this message and exit.

Empty file added planemo/autopygen/__init__.py
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