Add test

artis-mcrt · Dec 17, 2024 · 72f120a · 72f120a
1 parent 6c447b7
commit 72f120a
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Showing 10 changed files with 55 additions and 48 deletions.
diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -32,14 +32,6 @@ jobs:
               run: |
                   python -m pip install -e .
 
-            - name: Lint with flake8
-              working-directory: artisatomic/
-              run: |
-                  # stop the build if there are Python syntax errors or undefined names
-                  flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-                  # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-                  flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
             - name: Lint with mypy
               run: |
                   mypy --install-types --non-interactive
@@ -97,7 +89,7 @@ jobs:
     tests:
         strategy:
             matrix:
-                testname: [cmfgen, jplt]
+                testname: [cmfgen, jplt, floers25]
             fail-fast: false
 
         runs-on: macos-15
@@ -152,6 +144,16 @@ jobs:
                   cp tests/${{ matrix.testname }}/artisatomicionhandlers.json .
                   makeartisatomicfiles -output_folder tests/${{ matrix.testname }}/output
 
+            - name: Extract Floers25 atomic data
+              if: matrix.testname == 'floers25'
+              working-directory: atomic-data-floers25/
+              run: tar -zxvf testdata.tar.xz
+
+            - name: Generate artis atomic data files
+              run: |
+                  cp tests/${{ matrix.testname }}/artisatomicionhandlers.json .
+                  makeartisatomicfiles -output_folder tests/${{ matrix.testname }}/output
+
             - name: Checksum output files
               working-directory: tests/${{ matrix.testname }}/output
               run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -30,11 +30,6 @@ repos:
           - id: ruff
             args: [--fix]
           - id: ruff-format
-    - repo: https://github.com/pycqa/flake8
-      rev: 7.1.1
-      hooks:
-          - id: flake8
-            types: [python]
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v1.13.0
       hooks:

diff --git a/artisatomic/readfloers25data.py b/artisatomic/readfloers25data.py
@@ -6,41 +6,44 @@
 
 import artisatomic
 
-# from astropy import units as u
-# import os.path
-# import pandas as pd
-# from carsus.util import parse_selected_species
 
-BASEPATH = Path(Path.home() / "Google Drive/Shared drives/Atomic Data Group/FloersOpacityPaper/OutputFiles")
+def get_basepath() -> Path:
+    return artisatomic.PYDIR / ".." / "atomic-data-floers25" / "OutputFiles"
 
 
 def extend_ion_list(ion_handlers, calibrated=True):
+    BASEPATH = get_basepath()
     assert BASEPATH.is_dir()
-    handlername = "floers25" + "calib" if calibrated else "uncalib"
-    for s in BASEPATH.glob("*_levels_calib.txt"):
-        ionstr = s.name.lstrip("0123456789").split("_")[0]
-        elsym = ionstr.rstrip("IVX")
-        ion_stage_roman = ionstr.removeprefix(elsym)
-        atomic_number = artisatomic.elsymbols.index(elsym)
-
-        ion_stage = artisatomic.roman_numerals.index(ion_stage_roman)
-
-        found_element = False
-        for tmp_atomic_number, list_ions in ion_handlers:
-            if tmp_atomic_number == atomic_number:
-                if ion_stage not in [x[0] if len(x) > 0 else x for x in list_ions]:
-                    list_ions.append((ion_stage, handlername))
-                    list_ions.sort()
-                found_element = True
-        if not found_element:
-            ion_handlers.append(
-                (
-                    atomic_number,
-                    [(ion_stage, handlername)],
+    # if calibrated is requested, also add uncalibrated data where calibrated data is not available
+    calibflags = [True, False] if calibrated else [False]
+    for searchcalib in calibflags:
+        calibstr = "calib" if searchcalib else "uncalib"
+        handlername = f"floers25{calibstr}"
+        for s in BASEPATH.glob(f"*_levels_{calibstr}.txt*"):
+            ionstr = s.name.lstrip("0123456789").split("_")[0]
+            elsym = ionstr.rstrip("IVX")
+            ion_stage_roman = ionstr.removeprefix(elsym)
+            atomic_number = artisatomic.elsymbols.index(elsym)
+
+            ion_stage = artisatomic.roman_numerals.index(ion_stage_roman)
+
+            found_element = False
+            for tmp_atomic_number, list_ions in ion_handlers:
+                if tmp_atomic_number == atomic_number:
+                    if ion_stage not in [x[0] if len(x) > 0 else x for x in list_ions]:
+                        list_ions.append((ion_stage, handlername))
+                        list_ions.sort()
+                    found_element = True
+            if not found_element:
+                ion_handlers.append(
+                    (
+                        atomic_number,
+                        [(ion_stage, handlername)],
+                    )
                 )
-            )
 
     ion_handlers.sort(key=lambda x: x[0])
+
     return ion_handlers
 
 
@@ -64,13 +67,14 @@ def read_levels_and_transitions(atomic_number: int, ion_stage: int, flog, calibr
     ion_stage_roman = artisatomic.roman_numerals[ion_stage]
     calibstr = "calib" if calibrated else "uncalib"
 
+    BASEPATH = get_basepath()
     ionstr = f"{atomic_number}{elsym}{ion_stage_roman}"
     levels_file = BASEPATH / f"{ionstr}_levels_{calibstr}.txt"
     lines_file = BASEPATH / f"{ionstr}_transitions_{calibstr}.txt"
 
     artisatomic.log_and_print(
         flog,
-        f"Reading Floers+25 {calibstr}rated data for Z={atomic_number} ion_stage {ion_stage} ({elsym} {ion_stage_roman})",
+        f"Reading Floers+25 {calibstr}rated data for Z={atomic_number} ion_stage {ion_stage} ({elsym} {ion_stage_roman}) from {levels_file.name} and {lines_file.name}",
     )
 
     ionization_energy_in_ev = artisatomic.get_nist_ionization_energies_ev()[(atomic_number, ion_stage)]

diff --git a/atomic-data-floers25/.gitignore b/atomic-data-floers25/.gitignore
@@ -0,0 +1 @@
+OutputFiles
diff --git a/atomic-data-floers25/readme.txt b/atomic-data-floers25/readme.txt
@@ -0,0 +1,4 @@
+Suggested method is either copy or symlink the data to a subfolder called "OutputFiles"
+
+e.g.
+ln -s ~/Google\ Drive/Shared\ drives/Atomic\ Data\ Group/FloersOpacityPaper/OutputFiles OutputFiles
diff --git a/atomic-data-floers25/testdata.tar.xz b/atomic-data-floers25/testdata.tar.xz
diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,6 @@
 argcomplete>=3.5.1
 astropy>=6.1.4
 ChiantiPy>=0.15.1
-flake8>=6.1.0
 h5py>=3.10.0
 matplotlib>=3.9.2
 mypy>=1.13.0

diff --git a/tests/floers25/artisatomicionhandlers.json b/tests/floers25/artisatomicionhandlers.json
@@ -0,0 +1,3 @@
+[
+    [66, [[3, "floersuncalib"]]]
+]
diff --git a/tests/floers25/checksums.txt b/tests/floers25/checksums.txt
@@ -0,0 +1,4 @@
+1305990e95d64971cad693ecaf27305f  adata.txt
+e19eb2c4a80a6dd70b7be8bdc045d030  compositiondata.txt
+a673d82823ddddbb9b26ef8c8e6aed28  phixsdata_v2.txt
+1f22937fa04c26bae7c170674ccc2513  transitiondata.txt