Fix compatability (#148)

* remove depracated likelihood.theory calls * codestyle * sphinx compatability update * sphinx compatability update 2204 * add build tools * move rtd python ver * rtd try different pyver * rtd try different order * conda on rtd * update rtd mock import * add rtd theme * add rtd theme correctly * add rtd theme in setup.cfg * Testing yaml instead of yml. * added docs conda env * add full requirements in docs * pin tensorflow dep --------- Co-authored-by: Hidde Jense <JenseH@cardiff.ac.uk>
simonsobs · Oct 24, 2023 · 3075927 · 3075927
1 parent d293248
commit 3075927
Show file tree

Hide file tree

Showing 13 changed files with 83 additions and 42 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,20 @@
+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "miniconda3-4.7"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+# python:
+#   install:
+#     - requirements: docs/requirements.txt
+#     - method: pip
+#       path: .
+
+conda:
+  environment: docs/soliket-docs.yml
+
+formats: all
diff --git a/.readthedocs.yml b/.readthedocs.yml
diff --git a/docs/conf.py b/docs/conf.py
@@ -8,7 +8,7 @@
 sys.path.insert(0, "..")
 
 # Create some mock imports
-import mock
+from unittest import mock
 MOCK_MODULES = ["cosmopower", "tensorflow", "pyccl", "camb"]
 for module in MOCK_MODULES:
     sys.modules[module] = mock.Mock()

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1 +1,20 @@
+numpy
+scipy
+pandas
+scikit-learn
+pyyaml
+py-bobyqa
+packaging
+tqdm
+portalocker
+dill
+fuzzywuzzy
+astropy
+getdist
+cobaya
+pyccl
+sacc
+fgspectra>=1.1.0
+syslibrary
 sphinx>=4.0
+sphinx_rtd_theme
diff --git a/docs/soliket-docs.yml b/docs/soliket-docs.yml
@@ -0,0 +1,19 @@
+name: soliket-docs
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - python>=3.8,<3.11
+  - pip
+  - pytest-cov
+  - compilers
+  - make
+  - cmake
+  - swig
+  - gsl
+  - fftw
+  - cython
+  - mpi4py
+  - camb
+  - pip:
+      - -r requirements.txt
diff --git a/requirements.txt b/requirements.txt
@@ -6,6 +6,7 @@ pyyaml
 py-bobyqa
 packaging
 tqdm
+tensorflow<2.14
 portalocker
 dill
 fuzzywuzzy

diff --git a/setup.cfg b/setup.cfg
@@ -36,6 +36,7 @@ all =
     cosmopower
 docs =
     sphinx
+    sphinx_rtd_theme
 
 [flake8]
 select = E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,

diff --git a/soliket/ccl.py b/soliket/ccl.py
@@ -70,7 +70,7 @@
 * ``fsigma8``
 * ``sigma8_z``
 
-Then, to obtain the results, evaluate the contents of ``self.theory.get_CCL()`` in
+Then, to obtain the results, evaluate the contents of ``self.provider.get_CCL()`` in
 the likelihood.
 """
 

diff --git a/soliket/clusters/clusters.py b/soliket/clusters/clusters.py
@@ -104,31 +104,31 @@ def _get_catalog(self):
         return df
 
     def _get_om(self):
-        return (self.theory.get_param("omch2") + self.theory.get_param("ombh2")) / (
-            (self.theory.get_param("H0") / 100.0) ** 2
+        return (self.provider.get_param("omch2") + self.provider.get_param("ombh2")) / (
+            (self.provider.get_param("H0") / 100.0) ** 2
         )
 
     def _get_ob(self):
-        return (self.theory.get_param("ombh2")) / (
-            (self.theory.get_param("H0") / 100.0) ** 2
+        return (self.provider.get_param("ombh2")) / (
+            (self.provider.get_param("H0") / 100.0) ** 2
         )
 
     def _get_Ez(self):
-        return self.theory.get_Hubble(self.zarr) / self.theory.get_param("H0")
+        return self.provider.get_Hubble(self.zarr) / self.provider.get_param("H0")
 
     def _get_Ez_interpolator(self):
         return interp1d(self.zarr, self._get_Ez())
 
     def _get_DAz(self):
-        return self.theory.get_angular_diameter_distance(self.zarr)
+        return self.provider.get_angular_diameter_distance(self.zarr)
 
     def _get_DAz_interpolator(self):
         return interp1d(self.zarr, self._get_DAz())
 
     def _get_HMF(self):
-        h = self.theory.get_param("H0") / 100.0
+        h = self.provider.get_param("H0") / 100.0
 
-        Pk_interpolator = self.theory.get_Pk_interpolator(
+        Pk_interpolator = self.provider.get_Pk_interpolator(
             ("delta_nonu", "delta_nonu"), nonlinear=False
         ).P
         pks = Pk_interpolator(self.zarr, self.k)
@@ -137,7 +137,7 @@ def _get_HMF(self):
 
         Ez = (
             self._get_Ez()
-        )  # self.theory.get_Hubble(self.zarr) / self.theory.get_param("H0")
+        )  # self.provider.get_Hubble(self.zarr) / self.provider.get_param("H0")
         om = self._get_om()
 
         hmf = mf.HMF(om, Ez, pk=pks * h**3, kh=self.k / h, zarr=self.zarr)
@@ -153,7 +153,7 @@ def _get_param_vals(self, **kwargs):
         scat = 0.2
         massbias = 1.0
 
-        H0 = self.theory.get_param("H0")
+        H0 = self.provider.get_param("H0")
         ob = self._get_ob()
         om = self._get_om()
         param_vals = {
@@ -179,7 +179,7 @@ def _get_rate_fn(self, **kwargs):
 
         dn_dzdm_interp = HMF.inter_dndmLogm(delta=500)
 
-        h = self.theory.get_param("H0") / 100.0
+        h = self.provider.get_param("H0") / 100.0
 
         def Prob_per_cluster(z, tsz_signal, tsz_signal_err):
             c_y = tsz_signal
@@ -199,15 +199,15 @@ def Prob_per_cluster(z, tsz_signal, tsz_signal_err):
         # Implement a function that returns a rate function (function of (tsz_signal, z))
 
     def _get_dVdz(self):
-        DA_z = self.theory.get_angular_diameter_distance(self.zarr)
+        DA_z = self.provider.get_angular_diameter_distance(self.zarr)
 
         dV_dz = (
             DA_z**2
             * (1.0 + self.zarr) ** 2
-            / (self.theory.get_Hubble(self.zarr) / C_KM_S)
+            / (self.provider.get_Hubble(self.zarr) / C_KM_S)
         )
 
-        # dV_dz *= (self.theory.get_param("H0") / 100.0) ** 3.0  # was h0
+        # dV_dz *= (self.provider.get_param("H0") / 100.0) ** 3.0  # was h0
         return dV_dz
 
     def _get_n_expected(self, **kwargs):
@@ -223,7 +223,7 @@ def _get_n_expected(self, **kwargs):
 
         z_arr = self.zarr
 
-        h = self.theory.get_param("H0") / 100.0
+        h = self.provider.get_param("H0") / 100.0
 
         Ntot = 0
         dVdz = self._get_dVdz()
@@ -253,7 +253,7 @@ def _test_n_tot(self, **kwargs):
 
         z_arr = self.zarr
 
-        h = self.theory.get_param("H0") / 100.0
+        h = self.provider.get_param("H0") / 100.0
 
         Ntot = 0
         dVdz = self._get_dVdz()

diff --git a/soliket/mflike/mflike.py b/soliket/mflike/mflike.py
@@ -115,7 +115,7 @@ def _get_theory(self, **params_values):
         return self._get_power_spectra(cmbfg_dict)
 
     def logp(self, **params_values):
-        cmbfg_dict = self.theory.get_cmbfg_dict()
+        cmbfg_dict = self.provider.get_cmbfg_dict()
         return self.loglike(cmbfg_dict)
 
     def loglike(self, cmbfg_dict):

diff --git a/soliket/ps.py b/soliket/ps.py
@@ -13,7 +13,7 @@ def get_requirements(self):
         return {"Cl": {self.kind: self.lmax}}
 
     def _get_Cl(self):
-        return self.theory.get_Cl(ell_factor=True)
+        return self.provider.get_Cl(ell_factor=True)
 
     def _get_theory(self, **params_values):
         cl_theory = self._get_Cl()

diff --git a/soliket/tests/test_ccl.py b/soliket/tests/test_ccl.py
@@ -13,7 +13,7 @@ class CheckLike(Likelihood):
     a CCL object.
     """
     def logp(self, **params_values):
-        ccl = self.theory.get_CCL() # noqa F841
+        ccl = self.provider.get_CCL() # noqa F841
         return -1.0
 
     def get_requirements(self):

diff --git a/soliket/tests/test_xcorr.py b/soliket/tests/test_xcorr.py
@@ -95,7 +95,8 @@ def test_xcorr(theory):
 
     setup_chi_out = xcorr_lhood._setup_chi()
 
-    Pk_interpolator = xcorr_lhood.theory.get_Pk_interpolator(("delta_nonu", "delta_nonu"),
+    Pk_interpolator = xcorr_lhood.provider.get_Pk_interpolator(("delta_nonu",
+                                                                "delta_nonu"),
                                                              extrap_kmax=1.e8,
                                                              nonlinear=False).P