Resolving packages path with cobaya tools (#169)

* Fix extra letter in calibration params

* Use cobaya tools to resolve packages path

* flake

* Revert "flake"

This reverts commit 526acde.

* Update yaml files with correct paramnames and paths

For the `test_multi.py`, I switched from `MFLike` to `TestMFLike`, coherently with `test_mflike.py`

* Update paths in test_multi

* Enable multi and mflike in test_runs

* bug fix

* Avoid overwrite global packages_path

* flake

* Change pathfinding to data with packages path

* Revert to request forcing rootdir

* Point to `tox.ini` directory

---------

Co-authored-by: mgerbino <marti.gerbino@gmail.com>
Co-authored-by: Ian Harrison <itrharrison@gmail.com>

soliket/tests/test_bandpass.py

@@ -3,6 +3,7 @@
 from cobaya.model import get_model
 from ..constants import T_CMB, h_Planck, k_Boltzmann
 
+
 info = {"params": {
     "bandint_shift_LAT_93": 0.0,
     "bandint_shift_LAT_145": 0.0,

soliket/tests/test_cross_correlation.py

@@ -3,6 +3,7 @@
 from soliket.ccl import CCL
 from cobaya.model import get_model
 
+
 gammakappa_sacc_file = 'soliket/tests/data/des_s-act_kappa.toy-sim.sacc.fits'
 gkappa_sacc_file = 'soliket/tests/data/gc_cmass-actdr4_kappa.sacc.fits'
 
@@ -25,12 +26,12 @@
 }
 
 
-def test_galaxykappa_import(request):
+def test_galaxykappa_import():
 
     from soliket.cross_correlation import GalaxyKappaLikelihood # noqa F401
 
 
-def test_shearkappa_import(request):
+def test_shearkappa_import():
 
     from soliket.cross_correlation import ShearKappaLikelihood # noqa F401
 

soliket/tests/test_lensing.py

@@ -1,12 +1,9 @@
-import os
-import tempfile
 import numpy as np
 from cobaya.model import get_model
 
-packages_path = os.environ.get("COBAYA_PACKAGES_PATH") or os.path.join(
-    tempfile.gettempdir(), "lensing_packages"
-)
+from cobaya.tools import resolve_packages_path
 
+packages_path = resolve_packages_path()
 # Cosmological parameters for the test data from SO sims
 # See https://github.com/simonsobs/SOLikeT/pull/101 for validation plots
 fiducial_params = {
@@ -31,8 +28,14 @@ def test_lensing_import(request):
 def test_lensing_like(request):
 
     from cobaya.install import install
-    install({"likelihood": {"soliket.lensing.LensingLikelihood": None}},
-            path=packages_path, skip_global=False, force=True, debug=True)
+    install(
+        {"likelihood": {"soliket.lensing.LensingLikelihood": None}},
+        path=packages_path,
+        skip_global=False,
+        force=True,
+        debug=True,
+        no_set_global=True,
+    )
 
     from soliket.lensing import LensingLikelihood
 
@@ -49,8 +52,14 @@ def test_lensing_ccl_limber(request):
     """
 
     from cobaya.install import install
-    install({"likelihood": {"soliket.lensing.LensingLikelihood": None}},
-            path=packages_path, skip_global=False, force=True, debug=True)
+    install(
+        {"likelihood": {"soliket.lensing.LensingLikelihood": None}},
+        path=packages_path,
+        skip_global=False,
+        force=True,
+        debug=True,
+        no_set_global=True,
+    )
 
     from soliket.lensing import LensingLikelihood
     from copy import deepcopy

soliket/tests/test_mflike.py

@@ -2,17 +2,16 @@
 Make sure that this returns the same result as original mflike.MFLike from LAT_MFlike repo
 """
 import os
-import tempfile
 import unittest
 from packaging.version import Version
 
 import camb
 import soliket  # noqa
 from soliket.mflike import TestMFLike
 
-packages_path = os.environ.get("COBAYA_PACKAGES_PATH") or os.path.join(
-    tempfile.gettempdir(), "LAT_packages"
-)
+from cobaya.tools import resolve_packages_path
+
+packages_path = resolve_packages_path()
 
 cosmo_params = {
     "cosmomc_theta": 0.0104085,
@@ -77,8 +76,14 @@ class MFLikeTest(unittest.TestCase):
     def setUp(self):
         from cobaya.install import install
 
-        install({"likelihood": {"soliket.mflike.TestMFLike": None}},
-                path=packages_path, skip_global=False, force=True, debug=True)
+        install(
+            {"likelihood": {"soliket.mflike.TestMFLike": None}},
+            path=packages_path,
+            skip_global=False,
+            force=True,
+            debug=True,
+            no_set_global=True,
+        )
 
 
     def test_mflike(self):

soliket/tests/test_mflike.yaml

@@ -5,8 +5,7 @@ debug: True
 likelihood:
   soliket.mflike.TestMFLike:
     data_folder: TestMFLike
-    input_file: data_sacc_00044.fits
-    cov_Bbl_file: data_sacc_w_covar_and_Bbl.fits
+    input_file: test_data_sacc_00000.fits
     defaults:
       # Which spectra?
       polarizations: ['TT', 'TE', 'ET', 'EE']

soliket/tests/test_multi.py

@@ -1,17 +1,17 @@
 import numpy as np
-import pytest
 from soliket.tests.test_mflike import cosmo_params, nuisance_params
+from cobaya.tools import resolve_packages_path
 
+packages_path = resolve_packages_path()
 
-@pytest.mark.xfail(reason="lensing lhood install failure")
-def test_multi():
 
+def test_multi():
     lensing_options = {"theory_lmax": 5000}
 
-    pre = "data_sacc_"
+    pre = "test_data_sacc_"
     mflike_options = {
         "input_file": pre + "00000.fits",
-        "cov_Bbl_file": pre + "w_covar_and_Bbl.fits",
+        "data_folder": "TestMFLike",
         "stop_at_error": True,
     }
 
@@ -27,7 +27,7 @@ def test_multi():
     info = {
         "likelihood": {
             "soliket.gaussian.MultiGaussianLikelihood": {
-                "components": ["soliket.mflike.MFLike", "soliket.LensingLikelihood"],
+                "components": ["soliket.mflike.TestMFLike", "soliket.LensingLikelihood"],
                 "options": [mflike_options, lensing_options],
                 "stop_at_error": True,
             }
@@ -40,7 +40,7 @@ def test_multi():
     }
 
     info1 = {
-        "likelihood": {"soliket.mflike.MFLike": mflike_options},
+        "likelihood": {"soliket.mflike.TestMFLike": mflike_options},
         "theory": {"camb": camb_options,
                    "soliket.TheoryForge_MFLike": {'stop_at_error': True},
                    "soliket.Foreground": {"stop_at_error": True},

soliket/tests/test_multi.yaml

@@ -5,11 +5,11 @@ debug: True
 likelihood:
   soliket.gaussian.MultiGaussianLikelihood:
     components:
-      - soliket.mflike.MFLike
+      - soliket.mflike.TestMFLike
       - soliket.LensingLikelihood
     options:
-      - input_file: data_sacc_00044.fits
-        cov_Bbl_file: data_sacc_w_covar_and_Bbl.fits
+      - input_file: test_data_sacc_00000.fits
+        data_folder: "TestMFLike"
         defaults:
           # Which spectra?
           polarizations: ['TT', 'TE', 'ET', 'EE']
@@ -22,24 +22,19 @@ likelihood:
           symmetrize: False
         data:
           experiments:
-            LAT:
-              frequencies: [93, 145, 225]
+            - LAT_93
+            - LAT_145
+            - LAT_225
 
           spectra:
-            - experiments: ['LAT', 'LAT']
-              frequencies: [93, 93]
+            - experiments: ['LAT_93', 'LAT_93']
               polarizations: ['TT','TE','EE']
-            - experiments: ['LAT', 'LAT']
-              frequencies: [93, 145]
-            - experiments: ['LAT', 'LAT']
-              frequencies: [93, 225]
-            - experiments: ['LAT', 'LAT']
-              frequencies: [145, 145]
+            - experiments: ['LAT_93', 'LAT_145']
+            - experiments: ['LAT_93', 'LAT_225']
+            - experiments: ['LAT_145', 'LAT_145']
               polarizations: ['TT','TE','EE']
-            - experiments: ['LAT', 'LAT']
-              frequencies: [145, 225]
-            - experiments: ['LAT', 'LAT']
-              frequencies: [225, 225]
+            - experiments: ['LAT_145', 'LAT_225']
+            - experiments: ['LAT_225', 'LAT_225']
               polarizations: ['TT','TE','EE']
       - theory_lmax: 5000
         stop_at_error: true
@@ -187,43 +182,43 @@ params:
     proposal: 0.6
     latex: T_d
   # Systematics
-  bandint_shift_93:
+  bandint_shift_LAT_93:
     value: 0
     latex: \Delta_{\rm band}^{93}
-  bandint_shift_145:
+  bandint_shift_LAT_145:
     value: 0
     latex: \Delta_{\rm band}^{145}
-  bandint_shift_225:
+  bandint_shift_LAT_225:
     value: 0
     latex: \Delta_{\rm band}^{225}
-  calT_93:
+  calT_LAT_93:
     value: 1
     latex: \mathrm{Cal}_{\rm T}^{93}
-  calE_93:
+  calE_LAT_93:
     value: 1
     latex: \mathrm{Cal}_{\rm E}^{93}
-  calT_145:
+  calT_LAT_145:
     value: 1
     latex: \mathrm{Cal}_{\rm T}^{145}
-  calE_145:
+  calE_LAT_145:
     value: 1
     latex: \mathrm{Cal}_{\rm E}^{145}
-  calT_225:
+  calT_LAT_225:
     value: 1
     latex: \mathrm{Cal}_{\rm T}^{225}
-  calE_225:
+  calE_LAT_225:
     value: 1
     latex: \mathrm{Cal}_{\rm E}^{225}
   calG_all:
     value: 1
     latex: \mathrm{Cal}_{\rm G}^{\rm All}
-  alpha_93:
+  alpha_LAT_93:
     value: 0 #deg
     latex: \alpha^{93}
-  alpha_145:
+  alpha_LAT_145:
     value: 0 #deg
     latex: \alpha^{145}
-  alpha_225:
+  alpha_LAT_225:
     value: 0 #deg
     latex: \alpha^{225}
 

soliket/tests/test_runs.py

@@ -1,14 +1,10 @@
 import pkgutil
 import pytest
-import tempfile
 from cobaya.yaml import yaml_load
 from cobaya.run import run
+from cobaya.tools import resolve_packages_path
 
-import os
-
-packages_path = os.environ.get("COBAYA_PACKAGES_PATH") or os.path.join(
-    tempfile.gettempdir(), "lensing_packages"
-)
+packages_path = resolve_packages_path()
 
 
 @pytest.mark.parametrize("lhood",
@@ -21,18 +17,12 @@
                           # "xcorr"
                           ])
 def test_evaluate(lhood):
-    if lhood == "multi":
-        pytest.xfail(reason="multi lhood install failure")
-
-    if lhood == "mflike":
-        pytest.skip(reason="don't want to install 300Mb of data!")
-
     info = yaml_load(pkgutil.get_data("soliket", f"tests/test_{lhood}.yaml"))
     info["force"] = True
     info['sampler'] = {'evaluate': {}}
 
     from cobaya.install import install
-    install(info, path=packages_path, skip_global=True)
+    install(info, path=packages_path, skip_global=True, no_set_global=True)
 
     updated_info, sampler = run(info)
 
@@ -47,17 +37,11 @@ def test_evaluate(lhood):
                           # "xcorr"
                           ])
 def test_mcmc(lhood):
-    if lhood == "multi":
-        pytest.xfail(reason="multi lhood install failure")
-
-    if lhood == "mflike":
-        pytest.skip(reason="don't want to install 300Mb of data!")
-
     info = yaml_load(pkgutil.get_data("soliket", f"tests/test_{lhood}.yaml"))
     info["force"] = True
     info['sampler'] = {'mcmc': {'max_samples': 10, 'max_tries': 1000}}
 
     from cobaya.install import install
-    install(info, path=packages_path, skip_global=True)
+    install(info, path=packages_path, skip_global=True, no_set_global=True)
 
     updated_info, sampler = run(info)

tox.ini

@@ -47,8 +47,8 @@ extras =
 commands =
     pip freeze
     all: cobaya-install planck_2018_highl_plik.TTTEEE_lite_native --no-set-global
-    !cov: pytest -v --pyargs soliket {posargs}
-    cov: pytest -v --pyargs soliket --cov soliket --cov-report=xml --cov-config={toxinidir}/setup.cfg {posargs}
+    !cov: pytest -v --rootdir={toxinidir} --pyargs soliket {posargs}
+    cov: pytest -v --rootdir={toxinidir} --pyargs soliket --cov soliket --cov-report=xml --cov-config={toxinidir}/setup.cfg {posargs}
 
 [testenv:codestyle]
 skip_install = true