fixes for firecrown v.1.7.0

augur/analyze.py

@@ -128,7 +128,9 @@ def f(self, x, labels, pars_fid, sys_fid):
                 self.tools.reset()
                 self.lk.reset()
                 cosmo = ccl.Cosmology(**_pars)
-                self.lk.update(ParamsMap(_sys_pars))
+                pmap = ParamsMap(_sys_pars)
+                self.lk.update(pmap)
+                self.tools.update(pmap)
                 self.tools.prepare(cosmo)
                 f_out = self.lk.compute_theory_vector(self.tools)
             elif x.ndim == 2:
@@ -146,8 +148,10 @@ def f(self, x, labels, pars_fid, sys_fid):
                             raise ValueError(f'Parameter name {labels[j]} not recognized')
                     self.tools.reset()
                     self.lk.reset()
-                    self.lk.update(ParamsMap(_sys_pars))
+                    pmap = ParamsMap(_sys_pars)
+                    self.lk.update(pmap)
                     cosmo = ccl.Cosmology(**_pars)
+                    self.tools.update(pmap)
                     self.tools.prepare(cosmo)
                     f_out.append(self.lk.compute_theory_vector(self.tools))
             return np.array(f_out)
@@ -196,7 +200,7 @@ def compute_fisher_bias(self):
         # and the same length
         import os
         _calculate_biased_cls = True
-        _cls_fid = self.lk.measured_data_vector  # Get the fiducial data vector
+        _cls_fid = self.lk.get_data_vector()  # Get the fiducial data vector
 
         # Try to read the biased data vector
         if 'biased_dv' in self.config['fisher_bias']:

augur/generate.py

@@ -252,7 +252,7 @@ def generate_sacc_and_stats(config):
     return S, cosmo, stats, sys_params
 
 
-def generate(config, return_all_outputs=False, write_sacc=True, force_read=True):
+def generate(config, return_all_outputs=False, write_sacc=True):
     """
     Generate likelihood object and sacc file with fiducial cosmology
 
@@ -267,10 +267,7 @@ def generate(config, return_all_outputs=False, write_sacc=True, force_read=True)
         likelihood object.
     write_sacc : bool
         If `True` it writes a sacc file with fiducial data vector.
-    force_read : bool
-        If `True` it repopulates the likelihood data vector with the contents of the Sacc file
-        generated here. Note: For high-condition covariances where the Cholesky decomposition
-        fails, setting force_read to `True` may result in a `LinAlgError`.
+    
 
     Returns:
     -------
@@ -307,6 +304,7 @@ def generate(config, return_all_outputs=False, write_sacc=True, force_read=True)
     cosmo.compute_nonlin_power()
     tools = ModelingTools(pt_calculator=pt_calculator)
     lk.update(sys_params)
+    tools.update(sys_params)
     tools.prepare(cosmo)
     # Run the likelihood (to get the theory)
     lk.compute_loglike(tools)
@@ -320,7 +318,7 @@ def generate(config, return_all_outputs=False, write_sacc=True, force_read=True)
         st = st.statistic
         st.ready = False
         S.add_ell_cl(st.sacc_data_type, st.sacc_tracers[0], st.sacc_tracers[1],
-                     st.ell_or_theta_, st.predicted_statistic_)
+                     st.ell_or_theta_, st.get_theory_vector())
     if config['cov_options']['cov_type'] == 'gaus_internal':
         fsky = config['cov_options']['fsky']
         cov = get_gaus_cov(S, lk, cosmo, fsky, config)
@@ -382,9 +380,7 @@ def generate(config, return_all_outputs=False, write_sacc=True, force_read=True)
         print(config['fiducial_sacc_path'])
         S.save_fits(config['fiducial_sacc_path'], overwrite=True)
     # Update covariance and inverse -- TODO need to update cholesky!!
-    if force_read:
-        # Hacky way to overwrite...
-        lk.read(S)
-        lk.measured_data_vector = lk.get_data_vector()
+    lk = ConstGaussian(statistics=stats)
+    lk.read(S)
     if return_all_outputs:
         return lk, S, tools, sys_params

environment.yml

@@ -10,4 +10,4 @@ dependencies:
   - flake8
   - pip:
     - tjpcov
-  - qp
+  - qp-prob

pylintrc

@@ -0,0 +1,71 @@
+[MAIN]
+
+# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
+# number of processors available to use, and will cap the count on Windows to
+# avoid hangs.
+jobs=0
+
+# Minimum Python version to use for version dependent checks. Will default to
+# the version used to run pylint.
+py-version=3.9
+
+# Discover python modules and packages in the file system subtree.
+recursive=yes
+
+# Add custom pylint plugins
+# load-plugins=pylint_plugins.duplicate_code
+
+[MESSAGES CONTROL]
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=c-extension-no-member
+disable=too-few-public-methods
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME
+
+[BASIC]
+
+# Naming style matching correct argument names.
+argument-naming-style=any
+
+# Naming style matching correct attribute names.
+attr-naming-style=any
+
+# Naming style matching correct variable names.
+variable-naming-style=any
+
+# Naming style matching correct module level constants names.
+const-naming-style=any
+
+# Naming style matching correct method names.
+method-naming-style=any
+
+# Naming style matching correct function names.
+function-naming-style=any
+
+[STRING]
+
+# This flag controls whether inconsistent-quotes generates a warning when the
+# character used as a quote delimiter is used inconsistently within a module.
+check-quote-consistency=yes
+
+[TYPECHECK]
+
+# Tells whether to warn about missing members when the owner of the attribute
+# is inferred to be None.
+ignore-none=false
+
+[FORMAT]
+
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+expected-line-ending-format=LF
+
+[DESIGN]
+max-args=20
+max-attributes=20