Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PyEnzyme v2.0.0 #67

Draft
wants to merge 83 commits into
base: main
Choose a base branch
from
Draft
Changes from 1 commit
Commits
Show all changes
83 commits
Select commit Hold shift + click to select a range
e63345f
remove old workflows
JR-1991 Jun 22, 2024
71db8a1
fix spelling
JR-1991 Jun 22, 2024
fac2c87
remove unused code and artifacts
JR-1991 Jun 22, 2024
5dad733
add migrated lib
JR-1991 Jun 22, 2024
14f25a5
migrate to pyproject
JR-1991 Jun 22, 2024
6301617
linting and testing workflows
JR-1991 Jun 22, 2024
0c979c5
update fixtures
JR-1991 Jun 22, 2024
28697df
ignore mac things
JR-1991 Jun 22, 2024
a924ce6
fix typos
JR-1991 Jun 22, 2024
984847e
update readme
JR-1991 Jun 22, 2024
51ad12f
add new tests
JR-1991 Jun 22, 2024
7622a8a
only lint `pyenzyme` and `tests`
JR-1991 Jun 22, 2024
ab29d57
add dev examples
JR-1991 Jun 22, 2024
415ec1e
use `serialization_alias` for ld fields
JR-1991 Jun 25, 2024
c2e52e3
remove unused imports
JR-1991 Jun 25, 2024
0e7f516
added pyright and poetry
haeussma Jun 26, 2024
eb19c84
regenerated lib via gen.toml including celsius
haeussma Jun 26, 2024
bf0ff6d
replaced content with newly generated model
haeussma Jun 26, 2024
cf1618c
replaced mode, added celsius as unit
haeussma Jun 26, 2024
b2bb4f1
remove unused import
JR-1991 Jun 26, 2024
e8d6dc5
Merge pull request #68 from EnzymeML/add-celsius
JR-1991 Jun 26, 2024
065d66c
updated pandas dependency version range
haeussma Aug 16, 2024
981ddcb
update dev examples
JR-1991 Aug 16, 2024
ef42fa7
implement sbml omex parser
JR-1991 Aug 16, 2024
16f4e89
adjust serializer to model change
JR-1991 Aug 16, 2024
81dde6d
adjust and extend mappings to model changes
JR-1991 Aug 16, 2024
6b29053
format strings in multiple lines
JR-1991 Aug 16, 2024
7be7ace
model update
JR-1991 Aug 16, 2024
4890eb2
utilities to parse RDF
JR-1991 Aug 16, 2024
4fcdb6d
remove redundant `unit` arg
JR-1991 Aug 16, 2024
abe6944
export vital sbml functions
JR-1991 Aug 16, 2024
7350377
adjust to model changes
JR-1991 Aug 16, 2024
877cd41
add parameter fetcher
JR-1991 Aug 16, 2024
0e41499
refactor and extend to nested and multiple types
JR-1991 Aug 16, 2024
b15e149
rename to prevent mutability issues
JR-1991 Aug 16, 2024
6acea11
add `pymetadata` dep for OMEX support
JR-1991 Aug 16, 2024
d687c43
update tests
JR-1991 Aug 16, 2024
734f849
remove unused imports
JR-1991 Aug 16, 2024
df6c1af
remove unused `units`
JR-1991 Aug 16, 2024
835e2c3
update dev example
JR-1991 Aug 19, 2024
978e100
attach readers and writers to model class
JR-1991 Aug 19, 2024
ec497a5
add parameters to enzmldoc
JR-1991 Aug 19, 2024
165eeec
move params to root
JR-1991 Aug 19, 2024
c2c68c3
adapt to parameter loc and cast `str` to `float`
JR-1991 Aug 19, 2024
f1eeaf4
adapt parameter change
JR-1991 Aug 19, 2024
7547872
cast to float
JR-1991 Aug 19, 2024
958b321
add utility to strip ld keys
JR-1991 Aug 19, 2024
a57a732
update tests
JR-1991 Aug 19, 2024
6330f0c
add `to_pandas` to `EnzymeMLDocument`
JR-1991 Aug 20, 2024
bf62d86
data, time, time_unit in `MeasurementData` not mandatory anymore
haeussma Aug 20, 2024
fe3d3bb
- can not assume filenames
fbergmann Aug 23, 2024
f17303f
- init defaults to add missing attributes
fbergmann Aug 23, 2024
ca68f4f
- omex uses /tab-separated-values for tsv
fbergmann Aug 23, 2024
c895c26
update dev examples
JR-1991 Sep 7, 2024
2c9a3cf
add default imports
JR-1991 Sep 7, 2024
428a889
extract all files within omex
JR-1991 Sep 7, 2024
7a381d8
adapt parser and serializer to annotations
JR-1991 Sep 7, 2024
767c10a
add support for legacy and new version
JR-1991 Sep 7, 2024
8697431
rename method and update docs
JR-1991 Sep 7, 2024
43f76e6
use `float` instead of `int`
JR-1991 Sep 7, 2024
20e73a1
add function to extract the namespaces
JR-1991 Sep 7, 2024
64b2075
update tests
JR-1991 Sep 7, 2024
19f9281
add `pydantic-xml` dep
JR-1991 Sep 7, 2024
8e234dd
add testing section
JR-1991 Sep 7, 2024
93713f0
add container test
JR-1991 Sep 7, 2024
7830cd8
check fragments instead of complete uris
JR-1991 Sep 7, 2024
6d17141
Merge branch 'pydantic-xml' into v2-migration
JR-1991 Sep 7, 2024
64cd210
if multiplier is `1` set it to `None`
JR-1991 Sep 7, 2024
1e3bee5
add run command
JR-1991 Sep 7, 2024
2b702a2
add `vessel_id` to `Complex`
JR-1991 Sep 8, 2024
5d351a5
update dev examples
JR-1991 Sep 8, 2024
55eac11
extract compartment for `Complex`
JR-1991 Sep 8, 2024
f530e1e
update tests
JR-1991 Sep 8, 2024
2c10d54
remove unused import
JR-1991 Sep 8, 2024
91b9993
add suite class
JR-1991 Sep 23, 2024
de446b6
fix units not recognized
JR-1991 Sep 24, 2024
4efc6d1
Return `None` if `unit` is `None`
JR-1991 Sep 24, 2024
a0282d4
set temp unit and value optional
JR-1991 Sep 24, 2024
d1fa04e
fix unit ids not retrieved corectly
JR-1991 Sep 25, 2024
7e41492
fix unit ids and remove validation error
JR-1991 Sep 25, 2024
ccf56c4
Update pyproject.toml
haeussma Dec 18, 2024
c286783
Update pyproject.toml
haeussma Dec 19, 2024
c27bb23
Update pyproject.toml
haeussma Feb 7, 2025
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
model update
JR-1991 committed Aug 16, 2024
commit 7be7ace3cf4dcabeb72c1f14f0a9a301818a7ac4
Loading