Merge pull request #454 from PEtab-dev/develop

Release 0.1.8

Author: yannikschaelte

.github/workflows/ci_tests.yml

@@ -1,4 +1,4 @@
-name: CI tests
+name: CI
 
 # trigger
 on: [push]
@@ -8,30 +8,38 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6]
+        python-version: [3.8]
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v2
+
     - name: Prepare python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Cache pip
+
+    - name: Cache
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-${{ hashFiles('**/.ci_pip_reqs.txt') }}-${{ hashFiles('**/setup.py') }}
         restore-keys: |
           ${{ runner.os }}-
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r .ci_pip_reqs.txt
         pip install -e .[reports,combine]
+
     - name: Run tests
       run: |
-        pytest --cov
+        pytest --cov --cov-report=xml tests
         python -m flake8 --exclude=build,doc,example,tmp --extend-ignore=F403,F405
+
     - name: Coverage
-      run: codecov -t ${{ secrets.CODECOV_TOKEN }}
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml

CHANGELOG.md

@@ -2,6 +2,32 @@
 
 ## 0.1 series
 
+
+### 0.1.8
+
+Library:
+
+* Use ``core.is_empty`` to check for empty values (#434)
+* Move tests to python 3.8 (#435)
+* Update to libcombine 0.2.6 (#437)
+* Make float parsing from CSV round-trip (#444)
+* Lint: Allow model time in observable formulas (#445)
+* Lint: Detect duplicated observable ids (#446)
+* Fix likelihood calculation with missing values (#451)
+
+Documentation:
+
+* Move format documentation to restructuredtext format (#452)
+* Document all noise distributions and observable scales (#452)
+* Fix documentation for prior distribution (#449)
+
+Visualization:
+
+* Make XValue column non-mandatory (#429)
+* Apply correct condition sorting (#430)
+* Apply correct default x label (#431)
+
+
 ### 0.1.7
 
 Documentation:

README.md

@@ -105,7 +105,7 @@ Legend:
 ## Using PEtab
 
 If you would like to use PEtab yourself, please have a look at 
-[doc/documentation_data_format.md](doc/documentation_data_format.md) or at
+[doc/documentation_data_format.rst](doc/documentation_data_format.rst) or at
 the example models provided in the 
 [benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).