Merge branch 'master' into test_new_EFIT_mappings_for_IDA

.github/workflows/regression.yml

@@ -15,14 +15,25 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
+      matrix:
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+    # 3.12 does not yet work because numpy removed numpy.distutils that pygacode relies on
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.6'
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+
+    - name: Extra dependencies required for 3.7
+      if: ${{matrix.python-version == '3.7'}}
+      run: |
+        sudo apt-get update
+        sudo apt-get install libhdf5-dev libnetcdf-dev
 
     - name: Install numpy
       run: |
@@ -32,7 +43,18 @@ jobs:
       run: |
         python3 -m pip install -r requirements.txt
 
-    - name: Install OMAS
+    # numpy is a build time dependency of pygacode
+    # but before pygacode 1.0 it did not specify its build dependencies correctly
+    # and pygacode requires python >= 3.8,
+    # so for 3.7 we need to build without build isolation and manually install numpy
+    - name: Install OMAS (Py 3.7)
+      if: ${{matrix.python-version == '3.7'}}
+      run: |
+        python3 -m pip install wheel
+        python3 -m pip install --no-build-isolation .[machine]
+
+    - name: Install OMAS (normal)
+      if: ${{matrix.python-version != '3.7'}}
       run: |
         python3 -m pip install .[machine]
 

.github/workflows/stale.yml

@@ -10,10 +10,22 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@v3
+    - uses: actions/stale@v9
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-issue-message: 'Stale issue message'
-        stale-pr-message: 'Stale pull request message'
+        # Do not mark issues with these labels
+        exempt-issue-labels: "bug,enhancement,WIP"
+        stale-issue-message: >
+            This issue has not seen any activity in the past 60 days.
+            It is now marked as stale and will be closed in 7 days if
+            no further activity is registered.
+        # Do not mark PRs with these labels
+        exempt-pr-labels: 'WIP,Blocked-by-other-PR'
+        stale-pr-message: >
+            This PR has not seen any activity in the past 60 days.
+            It is now marked as stale and will be closed in 7 days if
+            no further activity is registered.
         stale-issue-label: 'no-issue-activity'
         stale-pr-label: 'no-pr-activity'
+        days-before-stale: 60
+        days-before-close: 21

Makefile

@@ -100,7 +100,7 @@ testpypi:
 hash:
 	pip hash dist/omas-$(VERSION).tar.gz
 
-release: tests requirements json cocos docs tag
+release: test requirements json cocos docs tag
 	@echo 'Make release done'
 
 fmt:

README.md

@@ -1,5 +1,5 @@
 ![OMAS version](https://img.shields.io/github/tag-date/gafusion/omas.svg?label=OMAS&color=blue)
-![IMAS version](https://img.shields.io/badge/IMAS-3.39.0-yellow)
+![IMAS version](https://img.shields.io/badge/IMAS-3.41.0-yellow)
 
 ![GitHub repo size](https://img.shields.io/github/repo-size/gafusion/omas.svg?color=blue)
 

omas/examples/connect_gkdb.py

@@ -15,8 +15,8 @@
 # load a sample GKDB sample json file
 sample_filename = omas_dir + 'samples/gkdb_linear_eigenvalue.json'
 ods = ODS()
-# warn about `gyrokinetics.fluxes_integrated_norm = []` and drop it
-ods['gyrokinetics'].load(sample_filename, consistency_check='warn_drop')
+# warn about `gyrokinetics_local.fluxes_integrated_norm = []` and drop it
+ods['gyrokinetics_local'].load(sample_filename, consistency_check='warn_drop')
 
 # show content
 pprint(ods.pretty_paths())
@@ -29,11 +29,11 @@
 
     __file__ = inspect.getfile(lambda: None)
 filename = omas_testdir(__file__) + '/gkdb_linear_initialvalue.json'
-ods['gyrokinetics'].save(filename)
+ods['gyrokinetics_local'].save(filename)
 
 # load the newly saved copy
 ods1 = ODS()
-ods1['gyrokinetics'].load(filename)
+ods1['gyrokinetics_local'].load(filename)
 
 # look for differences between original GKDB json and OMAS json
 differences = ods.diff(ods1, ignore_type=True)

omas/examples/omas_mongo_example.py

@@ -44,8 +44,8 @@
 print('load a sample GKDB sample json file')
 sample_filename = omas_dir + 'samples/gkdb_linear_eigenvalue.json'
 ods = ODS()
-# warn about `gyrokinetics.fluxes_integrated_norm = []` and drop it
-ods['gyrokinetics'].load(sample_filename, consistency_check='warn_drop')
+# warn about `gyrokinetics_local.fluxes_integrated_norm = []` and drop it
+ods['gyrokinetics_local'].load(sample_filename, consistency_check='warn_drop')
 
 print('write GKDB entry to the database')
 _id = ods.save('mongo', collection='gkdb', database='test')

omas/examples/omas_units.py

@@ -31,7 +31,7 @@
 # how to manipulate data that has units
 ods.sample()
 with omas_environment(ods, unitsio=True):
-    ne = ods['core_profiles.profiles_1d.0.electrons.density']
+    ne = ods['core_profiles.profiles_1d.0.electrons.density_thermal']
     print(f'Mean density in  m^-3: {numpy.mean(ne.to("m^-3").magnitude):3.3g}')
     print(f'Mean density in cm^-3: {numpy.mean(ne.to("cm^-3").magnitude):3.3g}')