diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7855e7397..9a434d82e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -73,7 +73,7 @@ jobs:
run: .github/workflows/install_deps.sh amici pysb
- name: Run tests
- timeout-minutes: 25
+ timeout-minutes: 35
run: tox -e petab
- name: Coverage
@@ -166,15 +166,15 @@ jobs:
steps:
- name: Check out repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
- name: Prepare python ${{ matrix.python-version }}
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache
- uses: actions/cache@v1
+ uses: actions/cache@v3
with:
path: ~/.cache
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-hierarchical
diff --git a/.github/workflows/install_deps.sh b/.github/workflows/install_deps.sh
index 260d48628..09957e254 100755
--- a/.github/workflows/install_deps.sh
+++ b/.github/workflows/install_deps.sh
@@ -37,7 +37,7 @@ for par in "$@"; do
pysb)
# bionetgen
wget -q -O bionetgen.tar \
- https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.6.0/BioNetGen-2.6.0-linux.tgz
+ https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.8.5/BioNetGen-2.8.5-linux.tar.gz
tar -xf bionetgen.tar
;;
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 8724e6fc2..b51746437 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -6,6 +6,33 @@ Release notes
..........
+0.3.1 (2023-06-22)
+-------------------
+* Visualize:
+ * Parameter plot w/ hier. pars, noise estimation for splines (#1061)
+* Sampling:
+ * AdaptiveMetropolis failure fix for bounded priors (#1065)
+* Ensembles
+ * Speed up Ensemble from History (#1063)
+* PEtab support:
+ * Support for petab 0.2.x (#1073)
+ * Remove PetabImporterPysb #1082)
+* Objective
+ * AggregatedObjective: objective-specific kwargs for call_unprocessed (#1068)
+* Select
+ * Use predecessor stored in file (#1059)
+ * support petab-select version 0.1.8 (#1070)
+* Examples
+ * Synthetic data: update for libpetab-python v0.2.0 (#1060)
+ * Fix error in sampling_diagnostics which led to test failure(#1092)
+* General
+ * Test fixes (#1064)
+ * Fix numpy DeprecationWarnings (#1076)
+ * GHA: Fix deprecation warnings (#1075)
+ * Fixed bug on existing file and no overwrite (#1046)
+ * Fix error in bound checking (#1081)
+
+
0.3.0 (2023-05-02)
-------------------
diff --git a/doc/example/example_nonlinear_monotone.ipynb b/doc/example/example_nonlinear_monotone.ipynb
index 7604b9fef..9c5881d5c 100644
--- a/doc/example/example_nonlinear_monotone.ipynb
+++ b/doc/example/example_nonlinear_monotone.ipynb
@@ -46,7 +46,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
@@ -83,7 +83,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
@@ -105,7 +105,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 15,
"metadata": {},
"outputs": [
{
@@ -453,6 +453,153 @@
" display(petab_problem.measurement_df)"
]
},
+ {
+ "attachments": {},
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "To estimate the noise parameters of the nonlinear-monotone observables, those noise parameters in the `parameter.tsv` file have to have column entries `estimate` with value 1 and column entry `parameterType` with value `sigma`, as in case of using relative data:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " parameterId | \n",
+ " parameterName | \n",
+ " parameterScale | \n",
+ " lowerBound | \n",
+ " upperBound | \n",
+ " nominalValue | \n",
+ " estimate | \n",
+ " parameterType | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " | 0 | \n",
+ " K1 | \n",
+ " K1 | \n",
+ " lin | \n",
+ " -5.00000 | \n",
+ " 5.0 | \n",
+ " 0.04 | \n",
+ " 0 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " | 1 | \n",
+ " K2 | \n",
+ " K2 | \n",
+ " lin | \n",
+ " -5.00000 | \n",
+ " 5.0 | \n",
+ " 20.00 | \n",
+ " 0 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " | 2 | \n",
+ " K3 | \n",
+ " K3 | \n",
+ " log10 | \n",
+ " 0.10000 | \n",
+ " 100000.0 | \n",
+ " 4000.00 | \n",
+ " 1 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " | 3 | \n",
+ " K5 | \n",
+ " K5 | \n",
+ " log10 | \n",
+ " 0.00001 | \n",
+ " 100000.0 | \n",
+ " 0.10 | \n",
+ " 1 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " | 4 | \n",
+ " sd_Activity | \n",
+ " \\sigma_{activity} | \n",
+ " lin | \n",
+ " 0.00000 | \n",
+ " inf | \n",
+ " 1.00 | \n",
+ " 1 | \n",
+ " sigma | \n",
+ "
\n",
+ " \n",
+ " | 5 | \n",
+ " sd_Ybar | \n",
+ " \\sigma_{ybar} | \n",
+ " lin | \n",
+ " 0.00000 | \n",
+ " inf | \n",
+ " 1.00 | \n",
+ " 1 | \n",
+ " sigma | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "