Skip to content

Commit

Permalink
Update Pharmpy
Browse files Browse the repository at this point in the history
  • Loading branch information
@rikardn
rikardn committed Jan 15, 2025
1 parent 1430bf6 commit 0044f01
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion pharmpy
Submodule pharmpy updated 98 files
+3 −2 .github/workflows/deploy.yml
+13 −4 .github/workflows/integration.yml
+5 −5 .github/workflows/main.yml
+1 −1 .github/workflows/publish-docs.yml
+37 −0 CHANGELOG.rst
+1 −1 docs-requirements.txt
+6 −0 docs/amd.rst
+7 −7 docs/covsearch.rst
+12 −12 docs/drug_metabolite.rst
+14 −16 docs/iivsearch.rst
+3 −6 docs/iovsearch.rst
+1 −1 docs/mfl.rst
+13 −15 docs/modelsearch.rst
+30 −26 docs/pkpd.rst
+9 −9 docs/structsearch.rst
+12 −12 docs/tmdd.rst
+9 −9 lint-requirements.txt
+1 −1 pretest-requirements.txt
+22 −22 requirements.txt
+6 −3 scripts/update_tool_results.sh
+2 −0 src/pharmpy/__init__.py
+9 −0 src/pharmpy/basic/expr.py
+33 −0 src/pharmpy/basic/unit.py
+38 −33 src/pharmpy/cli.py
+3 −2 src/pharmpy/model/execution_steps.py
+9 −7 src/pharmpy/model/external/nlmixr/error_model.py
+23 −11 src/pharmpy/model/external/nlmixr/model.py
+13 −11 src/pharmpy/model/external/nlmixr/model_block.py
+5 −2 src/pharmpy/model/external/nonmem/parsing.py
+8 −0 src/pharmpy/model/external/nonmem/records/factory.py
+17 −2 src/pharmpy/model/external/nonmem/records/sizes_record.py
+28 −7 src/pharmpy/model/external/nonmem/update.py
+3 −2 src/pharmpy/model/random_variables.py
+13 −4 src/pharmpy/model/statements.py
+3 −2 src/pharmpy/modeling/allometry.py
+20 −20 src/pharmpy/modeling/error.py
+2 −1 src/pharmpy/modeling/estimation_steps.py
+6 −2 src/pharmpy/modeling/expressions.py
+7 −3 src/pharmpy/modeling/iterators.py
+2 −2 src/pharmpy/modeling/math.py
+4 −1 src/pharmpy/modeling/metabolite.py
+106 −92 src/pharmpy/modeling/odes.py
+8 −7 src/pharmpy/modeling/parameter_sampling.py
+25 −28 src/pharmpy/modeling/parameter_variability.py
+8 −8 src/pharmpy/modeling/pd.py
+6 −8 src/pharmpy/modeling/plots.py
+17 −14 src/pharmpy/modeling/results.py
+32 −30 src/pharmpy/modeling/tmdd.py
+2 −2 src/pharmpy/tools/allometry/tool.py
+46 −27 src/pharmpy/tools/amd/run.py
+1 −1 src/pharmpy/tools/common.py
+0 −542 src/pharmpy/tools/covsearch/forward.py
+1 −0 src/pharmpy/tools/covsearch/results.py
+1,179 −22 src/pharmpy/tools/covsearch/samba.py
+46 −45 src/pharmpy/tools/covsearch/tool.py
+1 −2 src/pharmpy/tools/external/dummy/run.py
+3 −1 src/pharmpy/tools/external/nonmem/results.py
+17 −14 src/pharmpy/tools/iivsearch/tool.py
+8 −8 src/pharmpy/tools/iovsearch/tool.py
+33 −12 src/pharmpy/tools/modelsearch/tool.py
+4 −10 src/pharmpy/tools/retries/tool.py
+9 −4 src/pharmpy/tools/run.py
+4 −4 src/pharmpy/tools/ruvsearch/tool.py
+2 −2 src/pharmpy/tools/simulation/__init__.py
+13 −1 src/pharmpy/tools/simulation/tool.py
+12 −13 src/pharmpy/tools/structsearch/pkpd.py
+6 −6 src/pharmpy/tools/structsearch/tool.py
+5 −2 src/pharmpy/workflows/args.py
+28 −2 src/pharmpy/workflows/contexts/baseclass.py
+2 −0 src/pharmpy/workflows/contexts/broadcasters/null.py
+11 −2 src/pharmpy/workflows/contexts/local_directory.py
+3 −0 src/pharmpy/workflows/contexts/null.py
+1 −1 src/pharmpy/workflows/dispatchers/local_dask/run.py
+1 −1 test-requirements.txt
+7 −0 tests/basic/test_expr.py
+20 −1 tests/basic/test_unit.py
+6 −1 tests/integration/test_common.py
+117 −9 tests/integration/test_covsearch.py
+12 −13 tests/integration/test_iivsearch.py
+5 −5 tests/integration/test_iovsearch.py
+33 −12 tests/integration/test_modelsearch.py
+5 −5 tests/integration/test_resume.py
+4 −4 tests/model/test_estimation.py
+10 −0 tests/model/test_statements.py
+1 −1 tests/nonmem/records/test_omega.py
+1 −1 tests/nonmem/records/test_theta.py
+1,166 −0 tests/testdata/nonmem/moxo_sim_data.csv
+1 −1 tests/testdata/results/amd_results.json
+14 −13 tests/tools/test_allometry.py
+19 −17 tests/tools/test_covsearch.py
+26 −15 tests/tools/test_iivsearch.py
+16 −15 tests/tools/test_iovsearch.py
+16 −12 tests/tools/test_modelsearch.py
+18 −15 tests/tools/test_run.py
+9 −20 tests/tools/test_ruvsearch.py
+20 −0 tests/tools/test_simulation.py
+9 −10 tests/tools/test_structsearch.py
+1 −1 tox.ini

0 comments on commit 0044f01

Please sign in to comment.