From 89dac9fa6afdbc574271aa9b450c2b9ffe2dd114 Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 09:42:56 +0000
Subject: [PATCH 01/11] add production rule for force process grouping

---
 validphys2/src/validphys/config.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/validphys2/src/validphys/config.py b/validphys2/src/validphys/config.py
index 9fd0977325..56598fcd5c 100644
--- a/validphys2/src/validphys/config.py
+++ b/validphys2/src/validphys/config.py
@@ -1358,6 +1358,9 @@ def produce_group_dataset_inputs_by_metadata(
     def produce_group_dataset_inputs_by_experiment(self, data_input):
         return self.produce_group_dataset_inputs_by_metadata(data_input, "experiment")
 
+    def produce_force_process_grouping(self, data_input):
+        return self.produce_group_dataset_inputs_by_metadata(data_input, "nnpdf31_process")
+
     def produce_scale_variation_theories(self, theoryid, point_prescription):
         """Produces a list of theoryids given a theoryid at central scales and a point
            prescription. The options for the latter are '3 point', '5 point', '5bar point', '7 point'

From 871f934c39599fb1a525b920553bf902eb788465 Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 09:53:14 +0000
Subject: [PATCH 02/11] get rid of unneccessary groups_index

---
 .../src/validphys/theorycovariance/output.py  | 66 ++++++++-----------
 1 file changed, 26 insertions(+), 40 deletions(-)

diff --git a/validphys2/src/validphys/theorycovariance/output.py b/validphys2/src/validphys/theorycovariance/output.py
index 819d501b4c..fc0f855210 100644
--- a/validphys2/src/validphys/theorycovariance/output.py
+++ b/validphys2/src/validphys/theorycovariance/output.py
@@ -76,7 +76,7 @@ def matrix_plot_labels(df):
     return ticklocs, ticklabels, startlocs
 
 
-def plot_covmat_heatmap(covmat, title, groups_index):
+def plot_covmat_heatmap(covmat, title):
     """Matrix plot of a covariance matrix."""
     df = covmat
     df.sort_index(0, inplace=True)
@@ -180,9 +180,9 @@ def _get_key(element):
 
 
 @figure
-def plot_corrmat_heatmap(corrmat, title, groups_index):
+def plot_corrmat_heatmap(corrmat, title):
     """Matrix plot of a correlation matrix"""
-    df = pd.DataFrame(corrmat.values, index=groups_index, columns=groups_index)
+    df = corrmat
     df.sort_index(0, inplace=True)
     df.sort_index(1, inplace=True)
     oldindex = df.index.tolist()
@@ -210,30 +210,29 @@ def plot_corrmat_heatmap(corrmat, title, groups_index):
 
 
 @figure
-def plot_normexpcovmat_heatmap(groups_normcovmat, groups_index):
+def plot_normexpcovmat_heatmap(groups_normcovmat):
     """Matrix plot of the experiment covariance matrix normalised to data."""
     fig = plot_covmat_heatmap(
-        groups_normcovmat, "Experimental Covariance Matrix", groups_index
+        groups_normcovmat, "Experimental Covariance Matrix"
     )
     return fig
 
 
 @figure
-def plot_expcorrmat_heatmap(groups_corrmat, groups_index):
+def plot_expcorrmat_heatmap(groups_corrmat):
     """Matrix plot of the experiment correlation matrix"""
     fig = plot_corrmat_heatmap(
-        groups_corrmat, "Experimental Correlation Matrix", groups_index
+        groups_corrmat, "Experimental Correlation Matrix"
     )
     return fig
 
 
 @figure
-def plot_normthblockcovmat_heatmap(theory_normblockcovmat, groups_index):
+def plot_normthblockcovmat_heatmap(theory_normblockcovmat):
     """Matrix plot for block diagonal theory covariance matrix"""
     fig = plot_covmat_heatmap(
         theory_normblockcovmat,
         "Block diagonal theory covariance matrix by dataset",
-        groups_index,
     )
     return fig
 
@@ -242,7 +241,6 @@ def plot_normthblockcovmat_heatmap(theory_normblockcovmat, groups_index):
 def plot_normthcovmat_heatmap_custom(
     theory_normcovmat_custom,
     theoryids,
-    groups_index,
     fivetheories: (str, type(None)) = None,
 ):
     """Matrix plot for block diagonal theory covariance matrix by process type"""
@@ -253,18 +251,17 @@ def plot_normthcovmat_heatmap_custom(
         elif fivetheories == "linear":
             l = "linear 5"
     fig = plot_covmat_heatmap(
-        theory_normcovmat_custom, f"Theory Covariance matrix ({l} pt)", groups_index
+        theory_normcovmat_custom, f"Theory Covariance matrix ({l} pt)"
     )
     return fig
 
 
 @figure
-def plot_thblockcorrmat_heatmap(theory_blockcorrmat, groups_index):
+def plot_thblockcorrmat_heatmap(theory_blockcorrmat):
     """Matrix plot of the theory correlation matrix"""
     fig = plot_corrmat_heatmap(
         theory_blockcorrmat,
-        "Theory correlation matrix block diagonal by dataset",
-        groups_index,
+        "Theory correlation matrix block diagonal by dataset"
     )
     return fig
 
@@ -273,7 +270,6 @@ def plot_thblockcorrmat_heatmap(theory_blockcorrmat, groups_index):
 def plot_thcorrmat_heatmap_custom(
     theory_corrmat_custom,
     theoryids,
-    groups_index,
     fivetheories: (str, type(None)) = None,
 ):
     """Matrix plot of the theory correlation matrix, correlations by process type"""
@@ -284,20 +280,18 @@ def plot_thcorrmat_heatmap_custom(
         elif fivetheories == "linear":
             l = "linear 5"
     fig = plot_corrmat_heatmap(
-        theory_corrmat_custom, f"Theory Correlation matrix ({l} pt)", groups_index
+        theory_corrmat_custom, f"Theory Correlation matrix ({l} pt)"
     )
     return fig
 
 
 @figure
 def plot_normexpplusblockthcovmat_heatmap(
-    experimentplusblocktheory_normcovmat, groups_index
-):
+    experimentplusblocktheory_normcovmat):
     """Matrix plot of the exp + theory covariance matrix normalised to data"""
     fig = plot_covmat_heatmap(
         experimentplusblocktheory_normcovmat,
         "Experiment + theory (block diagonal by dataset) covariance matrix",
-        groups_index,
     )
     return fig
 
@@ -306,7 +300,6 @@ def plot_normexpplusblockthcovmat_heatmap(
 def plot_normexpplusthcovmat_heatmap_custom(
     experimentplustheory_normcovmat_custom,
     theoryids,
-    groups_index,
     fivetheories: (str, type(None)) = None,
 ):
     """Matrix plot of the exp + theory covariance matrix normalised to data"""
@@ -318,19 +311,17 @@ def plot_normexpplusthcovmat_heatmap_custom(
             l = "linear 5"
     fig = plot_covmat_heatmap(
         experimentplustheory_normcovmat_custom,
-        f"Experimental + Theory Covariance Matrix ({l} pt)",
-        groups_index,
+        f"Experimental + Theory Covariance Matrix ({l} pt)"
     )
     return fig
 
 
 @figure
-def plot_expplusblockthcorrmat_heatmap(experimentplusblocktheory_corrmat, groups_index):
+def plot_expplusblockthcorrmat_heatmap(experimentplusblocktheory_corrmat):
     """Matrix plot of the exp + theory correlation matrix"""
     fig = plot_corrmat_heatmap(
         experimentplusblocktheory_corrmat,
         "Experiment + theory (block diagonal by dataset) correlation matrix",
-        groups_index,
     )
     return fig
 
@@ -339,7 +330,6 @@ def plot_expplusblockthcorrmat_heatmap(experimentplusblocktheory_corrmat, groups
 def plot_expplusthcorrmat_heatmap_custom(
     experimentplustheory_corrmat_custom,
     theoryids,
-    groups_index,
     fivetheories: (str, type(None)) = None,
 ):
     """Matrix plot of the exp + theory correlation matrix"""
@@ -351,14 +341,13 @@ def plot_expplusthcorrmat_heatmap_custom(
             l = "linear 5"
     fig = plot_corrmat_heatmap(
         experimentplustheory_corrmat_custom,
-        f"Experimental + Theory Correlation Matrix ({l} pt)",
-        groups_index,
+        f"Experimental + Theory Correlation Matrix ({l} pt)"
     )
     return fig
 
 
 @figure
-def plot_blockcovdiff_heatmap(theory_block_diag_covmat, groups_covmat, groups_index):
+def plot_blockcovdiff_heatmap(theory_block_diag_covmat, groups_covmat):
     """Matrix plot (thcov + expcov)/expcov"""
     df = (theory_block_diag_covmat.as_matrix() + groups_covmat.values) / np.mean(
         groups_covmat.values
@@ -366,8 +355,7 @@ def plot_blockcovdiff_heatmap(theory_block_diag_covmat, groups_covmat, groups_in
     fig = plot_covmat_heatmap(
         df,
         "(Theory + experiment)/mean(experiment)"
-        + "for block diagonal theory covmat by dataset",
-        groups_index,
+        + "for block diagonal theory covmat by dataset"
     )
     return fig
 
@@ -377,7 +365,6 @@ def plot_covdiff_heatmap_custom(
     theory_covmat_custom,
     groups_covmat,
     theoryids,
-    groups_index,
     fivetheories: (str, type(None)) = None,
 ):
     """Matrix plot (thcov + expcov)/expcov"""
@@ -391,8 +378,7 @@ def plot_covdiff_heatmap_custom(
     fig = plot_covmat_heatmap(
         df,
         "(Theory + experiment)/mean(experiment)"
-        + f"covariance matrices for {l} points",
-        groups_index,
+        + f"covariance matrices for {l} points"
     )
     return fig
 
@@ -403,7 +389,6 @@ def plot_diag_cov_comparison(
     groups_covmat,
     groups_data_values,
     theoryids,
-    groups_index,
     fivetheories: (str, type(None)) = None,
 ):
     """Plot of sqrt(cov_ii)/|data_i| for cov = exp, theory, exp+theory"""
@@ -414,19 +399,20 @@ def plot_diag_cov_comparison(
         elif fivetheories == "linear":
             l = "linear 5"
     data = np.abs(groups_data_values)
+    plot_index = theory_covmat_custom.index
     sqrtdiags_th = np.sqrt(np.diag(theory_covmat_custom)) / data
-    sqrtdiags_th = pd.DataFrame(sqrtdiags_th.values, index=groups_index)
+    sqrtdiags_th = pd.DataFrame(sqrtdiags_th.values, index=plot_index)
     sqrtdiags_th.sort_index(0, inplace=True)
     oldindex = sqrtdiags_th.index.tolist()
     newindex = sorted(oldindex, key=_get_key)
     sqrtdiags_th = sqrtdiags_th.reindex(newindex)
     sqrtdiags_exp = np.sqrt(np.diag(groups_covmat)) / data
-    sqrtdiags_exp = pd.DataFrame(sqrtdiags_exp.values, index=groups_index)
+    sqrtdiags_exp = pd.DataFrame(sqrtdiags_exp.values, index=plot_index)
     sqrtdiags_exp.sort_index(0, inplace=True)
     sqrtdiags_exp = sqrtdiags_exp.reindex(newindex)
     df_total = theory_covmat_custom + groups_covmat
     sqrtdiags_tot = np.sqrt(np.diag(df_total)) / data
-    sqrtdiags_tot = pd.DataFrame(sqrtdiags_tot.values, index=groups_index)
+    sqrtdiags_tot = pd.DataFrame(sqrtdiags_tot.values, index=plot_index)
     sqrtdiags_tot.sort_index(0, inplace=True)
     sqrtdiags_tot = sqrtdiags_tot.reindex(newindex)
     fig, ax = plt.subplots(figsize=(20, 10))
@@ -455,7 +441,6 @@ def plot_diag_cov_comparison(
 def plot_diag_cov_impact(
     theory_covmat_custom,
     groups_covmat,
-    groups_index,
     groups_data_values,
     theoryids,
     fivetheories: (str, type(None)) = None,
@@ -473,12 +458,13 @@ def plot_diag_cov_impact(
     inv_tot = (np.diag(la.inv(matrix_theory + matrix_experiment))) ** (
         -0.5
     ) / groups_data_values
-    df_inv_exp = pd.DataFrame(inv_exp, index=groups_index)
+    plot_index = theory_covmat_custom.index
+    df_inv_exp = pd.DataFrame(inv_exp, index=plot_index)
     df_inv_exp.sort_index(0, inplace=True)
     oldindex = df_inv_exp.index.tolist()
     newindex = sorted(oldindex, key=_get_key)
     df_inv_exp = df_inv_exp.reindex(newindex)
-    df_inv_tot = pd.DataFrame(inv_tot, index=groups_index)
+    df_inv_tot = pd.DataFrame(inv_tot, index=plot_index)
     df_inv_tot.sort_index(0, inplace=True)
     df_inv_tot = df_inv_tot.reindex(newindex)
     fig, ax = plt.subplots()

From dbe79ff005d8b68b157567d05bf13efaebb9316d Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 10:31:13 +0000
Subject: [PATCH 03/11] add procs actions

---
 validphys2/src/validphys/results.py | 36 +++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/validphys2/src/validphys/results.py b/validphys2/src/validphys/results.py
index 0d7d31c2d4..43a31f8353 100644
--- a/validphys2/src/validphys/results.py
+++ b/validphys2/src/validphys/results.py
@@ -154,6 +154,7 @@ def rawdata(self):
 
 experiments_data = collect("data", ("group_dataset_inputs_by_experiment",))
 
+procs_data = collect("data", ("force_process_grouping",))
 
 def groups_index(groups_data):
     """Return a pandas.MultiIndex with levels for group, dataset and point
@@ -193,17 +194,26 @@ def groups_index(groups_data):
 def experiments_index(experiments_data):
     return groups_index(experiments_data)
 
+def procs_index(procs_data):
+    return groups_index(procs_data)
 
 def groups_data_values(group_result_table):
     """Returns list of data values for the input groups."""
     data_central_values = group_result_table["data_central"]
     return data_central_values
 
+def procs_data_values(proc_result_table):
+    """Like groups_data_values but grouped by process."""
+    data_central_values = proc_result_table["data_central"]
+    return data_central_values
 
 groups_results = collect(
     "dataset_inputs_results", ("group_dataset_inputs_by_metadata",)
 )
 
+procs_results = collect(
+    "dataset_inputs_results", ("force_process_grouping",)
+)
 
 def group_result_table_no_table(groups_results, groups_index):
     """Generate a table containing the data central value, the central prediction,
@@ -243,12 +253,19 @@ def group_result_table(group_result_table_no_table):
     """Duplicate of group_result_table_no_table but with a table decorator."""
     return group_result_table_no_table
 
+def proc_result_table_no_table(procs_results, procs_index):
+    return group_result_table_no_table(procs_results, procs_index)
+
+@table
+def proc_result_table(proc_result_table_no_table):
+    return proc_result_table_no_table
 
 experiment_result_table = collect(
     "group_result_table", ("group_dataset_inputs_by_experiment",)
 )
 
 
+
 @table
 def group_result_table_68cl(
     groups_results, group_result_table_no_table: pd.DataFrame, pdf: PDF
@@ -334,6 +351,12 @@ def groups_covmat(groups_covmat_no_table):
     """Duplicate of groups_covmat_no_table but with a table decorator."""
     return groups_covmat_no_table
 
+def procs_covmat_no_table(experiments_covmat_no_table, procs_index):
+    return relabel_experiments_to_groups(experiments_covmat_no_table, procs_index)
+
+@table
+def procs_covmat(procs_covmat_no_table):
+    return procs_covmat_no_table
 
 experiments_sqrt_covmat = collect(
     "dataset_inputs_sqrt_covmat", ("group_dataset_inputs_by_experiment",)
@@ -401,6 +424,9 @@ def groups_normcovmat(groups_covmat, groups_data_values):
     mat = df / np.outer(groups_data_array, groups_data_array)
     return mat
 
+@table
+def procs_normcovmat(procs_covmat, procs_data_values):
+    return groups_normcovmat(procs_covmat, procs_data_values)
 
 @table
 def groups_corrmat(groups_covmat):
@@ -411,6 +437,9 @@ def groups_corrmat(groups_covmat):
     mat = diag_minus_half[:, np.newaxis] * df * diag_minus_half
     return mat
 
+@table
+def procs_corrmat(procs_covmat):
+    return groups_corrmat(procs_covmat)
 
 @table
 def closure_pseudodata_replicas(
@@ -1253,6 +1282,13 @@ def groups_central_values(group_result_table):
     central_theory_values = group_result_table["theory_central"]
     return central_theory_values
 
+def procs_central_values_no_table(proc_result_table):
+    central_theory_values = proc_result_table_no_table["theory_central"]
+    return central_theory_values
+
+@table
+def procs_central_values(proc_result_table):
+    return procs_central_values_no_table
 
 dataspecs_each_dataset_chi2 = collect("each_dataset_chi2", ("dataspecs",))
 each_dataset = collect("dataset", ("data",))

From ae91e6c532e99832c950e9bf936b4cc2c18fd306 Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 10:39:31 +0000
Subject: [PATCH 04/11] add procs_chi2_table

---
 validphys2/src/validphys/results.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/validphys2/src/validphys/results.py b/validphys2/src/validphys/results.py
index 43a31f8353..88028a7ec7 100644
--- a/validphys2/src/validphys/results.py
+++ b/validphys2/src/validphys/results.py
@@ -831,6 +831,9 @@ def groups_chi2_table(groups_data, pdf, groups_chi2, each_dataset_chi2):
     "groups_chi2_table", ("group_dataset_inputs_by_experiment",)
 )
 
+procs_chi2_table = collect(
+    "groups_chi2_table", ("force_process_grouping",)
+)
 
 @check_cuts_considered
 @table

From 76f5e9d782345aef899cd2b8ae6179c775986ab5 Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 10:48:04 +0000
Subject: [PATCH 05/11] replace groups -> process in thcov actions

---
 .../theorycovariance/construction.py          | 176 +++++++++---------
 .../src/validphys/theorycovariance/output.py  |  72 +++----
 2 files changed, 124 insertions(+), 124 deletions(-)

diff --git a/validphys2/src/validphys/theorycovariance/construction.py b/validphys2/src/validphys/theorycovariance/construction.py
index 94bddec505..65c8c30a82 100644
--- a/validphys2/src/validphys/theorycovariance/construction.py
+++ b/validphys2/src/validphys/theorycovariance/construction.py
@@ -15,19 +15,19 @@
 from reportengine.table import table
 from reportengine import collect
 
-from validphys.results import (groups_central_values, 
-                               groups_central_values_no_table, 
-                               groups_data_values)                              
+from validphys.results import (procs_central_values, 
+                               procs_central_values_no_table, 
+                               procs_data_values)                              
 from validphys.results import Chi2Data, results
 from validphys.calcutils import calc_chi2, all_chi2_theory, central_chi2_theory
 from validphys.theorycovariance.theorycovarianceutils import process_lookup, check_correct_theory_combination
 
 log = logging.getLogger(__name__)
 
-theoryids_groups_central_values = collect(groups_central_values,
+theoryids_procs_central_values = collect(procs_central_values,
                                                ('theoryids',))
 
-theoryids_groups_central_values_no_table = collect(groups_central_values_no_table,
+theoryids_procs_central_values_no_table = collect(procs_central_values_no_table,
                                                ('theoryids',))
 
 collected_theoryids = collect('theoryids',
@@ -51,14 +51,14 @@ def make_scale_var_covmat(predictions):
     return s
 
 @check_correct_theory_combination
-def theory_covmat_singleprocess_no_table(theoryids_groups_central_values_no_table,
-                           groups_index, theoryids,
+def theory_covmat_singleprocess_no_table(theoryids_procs_central_values_no_table,
+                           procs_index, theoryids,
                            fivetheories:(str, type(None)) = None):
 
     """Calculates the theory covariance matrix for scale variations.
-    The matrix is a dataframe indexed by groups_index."""
-    s = make_scale_var_covmat(theoryids_groups_central_values_no_table)
-    df = pd.DataFrame(s, index=groups_index, columns=groups_index)
+    The matrix is a dataframe indexed by procs_index."""
+    s = make_scale_var_covmat(theoryids_procs_central_values_no_table)
+    df = pd.DataFrame(s, index=procs_index, columns=procs_index)
     return df
 
 @table
@@ -70,7 +70,7 @@ def theory_covmat_singleprocess(theory_covmat_singleprocess_no_table,
 
 results_bytheoryids = collect(results,('theoryids',))
 each_dataset_results_bytheory = collect('results_bytheoryids',
-                                        ('group_dataset_inputs_by_metadata','data'))
+                                        ('force_process_grouping','data'))
 
 @check_correct_theory_combination
 def theory_covmat_datasets(each_dataset_results_bytheory,
@@ -117,46 +117,46 @@ def total_covmat_diagtheory_datasets(each_dataset_results_bytheory,
     return dataset_covmats
 
 @table
-def theory_block_diag_covmat(theory_covmat_datasets, groups_index):
+def theory_block_diag_covmat(theory_covmat_datasets, procs_index):
     """Takes the theory covariance matrices for individual datasets and
     returns a data frame with a block diagonal theory covariance matrix
     by dataset"""
     s  = la.block_diag(*theory_covmat_datasets)
-    df = pd.DataFrame(s, index=groups_index, columns=groups_index)
+    df = pd.DataFrame(s, index=procs_index, columns=procs_index)
     return df
 
 @table
-def theory_diagonal_covmat(theory_covmat_singleprocess_no_table, groups_index):
+def theory_diagonal_covmat(theory_covmat_singleprocess_no_table, procs_index):
     """Returns theory covmat with only diagonal values"""
     s = theory_covmat_singleprocess_no_table.values
     # Initialise array of zeros and set precision to same as FK tables
     s_diag = np.zeros((len(s),len(s)), dtype=np.float32)
     np.fill_diagonal(s_diag, np.diag(s))
-    df = pd.DataFrame(s_diag, index=groups_index, columns=groups_index)
+    df = pd.DataFrame(s_diag, index=procs_index, columns=procs_index)
     return df
 
-groups_results_theory = collect('groups_results', ('theoryids',))
+procs_results_theory = collect('procs_results', ('theoryids',))
 
 @check_correct_theory_combination
-def total_covmat_groups(groups_results_theory,
+def total_covmat_procs(procs_results_theory,
                              fivetheories:(str, type(None)) = None):
     """Same as total_covmat_datasets but per experiment rather than
     per dataset. Needed for calculation of chi2 per experiment."""
-    group_result_covmats = []
-    for group_result in zip(*groups_results_theory):
-        theory_centrals = [x[1].central_value for x in group_result]
+    proc_result_covmats = []
+    for proc_result in zip(*procs_results_theory):
+        theory_centrals = [x[1].central_value for x in proc_result]
         s = make_scale_var_covmat(theory_centrals)
-        sigma = group_result[0][0].covmat
+        sigma = proc_result[0][0].covmat
         cov = s + sigma
-        group_result_covmats.append(cov)
-    return group_result_covmats
+        proc_result_covmats.append(cov)
+    return proc_result_covmats
 
-commondata_groups = collect('commondata', ['group_dataset_inputs_by_metadata', 'data'])
+commondata_procs = collect('commondata', ['force_process_grouping', 'data'])
 
-def dataset_names(commondata_groups):
+def dataset_names(commondata_procs):
     """Returns a list of the names of the datasets, in the same order as
     they are inputted in the runcard"""
-    names = [commondata.name for commondata in commondata_groups]
+    names = [commondata.name for commondata in commondata_procs]
     return names
 
 ProcessInfo = namedtuple("ProcessInfo", ('theory', 'namelist', 'sizes'))
@@ -363,7 +363,7 @@ def covs_pt_prescrip(combine_by_type, process_starting_points, theoryids,
     return covmats
 
 @table
-def theory_covmat_custom(covs_pt_prescrip, covmap, groups_index):
+def theory_covmat_custom(covs_pt_prescrip, covmap, procs_index):
     """Takes the individual sub-covmats between each two processes and assembles
     them into a full covmat. Then reshuffles the order from ordering by process
     to ordering by experiment as listed in the runcard"""
@@ -378,17 +378,17 @@ def theory_covmat_custom(covs_pt_prescrip, covmap, groups_index):
     for i in range(matlength):
         for j in range(matlength):
             cov_by_exp[covmap[i]][covmap[j]] = mat[i][j]
-    df = pd.DataFrame(cov_by_exp, index=groups_index,
-                      columns=groups_index)
+    df = pd.DataFrame(cov_by_exp, index=procs_index,
+                      columns=procs_index)
     return df
 
 @check_correct_theory_combination
-def total_covmat_diagtheory_groups(groups_results_theory,
+def total_covmat_diagtheory_procs(procs_results_theory,
                                         fivetheories:(str, type(None)) = None):
-    """Same as total_covmat_datasets but per group rather than
-    per dataset. Needed for calculation of chi2 per group."""
+    """Same as total_covmat_datasets but per proc rather than
+    per dataset. Needed for calculation of chi2 per proc."""
     exp_result_covmats = []
-    for exp_result in zip(*groups_results_theory):
+    for exp_result in zip(*procs_results_theory):
         theory_centrals = [x[1].central_value for x in exp_result]
         s = make_scale_var_covmat(theory_centrals)
         # Initialise array of zeros and set precision to same as FK tables
@@ -423,131 +423,131 @@ def theory_corrmat_custom(theory_covmat_custom):
     return mat
 
 @table
-def theory_normcovmat_singleprocess(theory_covmat_singleprocess, groups_data_values):
+def theory_normcovmat_singleprocess(theory_covmat_singleprocess, procs_data_values):
     """Calculates the theory covariance matrix for scale variations normalised
     to data."""
     df = theory_covmat_singleprocess
-    mat = df/np.outer(groups_data_values, groups_data_values)
+    mat = df/np.outer(procs_data_values, procs_data_values)
     return mat
 
 @table
-def theory_normblockcovmat(theory_block_diag_covmat, groups_data_values):
+def theory_normblockcovmat(theory_block_diag_covmat, procs_data_values):
     """Calculates the theory covariance matrix for scale variations
     normalised to data, block diagonal by dataset."""
     df = theory_block_diag_covmat
-    mat = df/np.outer(groups_data_values, groups_data_values)
+    mat = df/np.outer(procs_data_values, procs_data_values)
     return mat
 
 @table
-def theory_normcovmat_custom(theory_covmat_custom, groups_data_values):
+def theory_normcovmat_custom(theory_covmat_custom, procs_data_values):
     """Calculates the theory covariance matrix for scale variations normalised
     to data, with variations according to the relevant prescription."""
     df = theory_covmat_custom
-    mat = df/np.outer(groups_data_values, groups_data_values)
+    mat = df/np.outer(procs_data_values, procs_data_values)
     return mat
 
 @table
-def experimentplustheory_covmat_singleprocess(groups_covmat_no_table,
+def experimentplustheory_covmat_singleprocess(procs_covmat_no_table,
                                                theory_covmat_singleprocess_no_table):
     """Calculates the experiment + theory covariance matrix for
     scale variations."""
-    df = groups_covmat_no_table + theory_covmat_singleprocess_no_table
+    df = procs_covmat_no_table + theory_covmat_singleprocess_no_table
     return df
 
 @table
-def experimentplusblocktheory_covmat(groups_covmat,
+def experimentplusblocktheory_covmat(procs_covmat,
                                       theory_block_diag_covmat):
     """Calculates the experiment + theory covariance
     matrix for scale variations."""
-    df = groups_covmat + theory_block_diag_covmat
+    df = procs_covmat + theory_block_diag_covmat
     return df
 
 @table
-def experimentplustheory_covmat_custom(groups_covmat,
+def experimentplustheory_covmat_custom(procs_covmat,
                                         theory_covmat_custom):
     """Calculates the experiment + theory covariance matrix for
     scale variations correlated according to the relevant prescription."""
-    df = groups_covmat + theory_covmat_custom
+    df = procs_covmat + theory_covmat_custom
     return df
 
 @table
-def experimentplustheory_normcovmat_singleprocess(groups_covmat,
+def experimentplustheory_normcovmat_singleprocess(procs_covmat,
                                      theory_covmat_singleprocess,
-                                     groups_data):
+                                     procs_data):
     """Calculates the experiment + theory covariance matrix for scale
        variations normalised to data."""
-    df = groups_covmat + theory_covmat_singleprocess
-    groups_data_array = np.array(groups_data)
-    mat = df/np.outer(groups_data_array, groups_data_array)
+    df = procs_covmat + theory_covmat_singleprocess
+    procs_data_array = np.array(procs_data)
+    mat = df/np.outer(procs_data_array, procs_data_array)
     return mat
 
 @table
-def experimentplusblocktheory_normcovmat(groups_covmat,
+def experimentplusblocktheory_normcovmat(procs_covmat,
                                           theory_block_diag_covmat,
-                                          groups_data_values,
+                                          procs_data_values,
                                           experimentplustheory_normcovmat):
     """Calculates the experiment + theory covariance matrix for scale
        variations normalised to data, block diagonal by data set."""
-    mat = experimentplustheory_normcovmat(groups_covmat,
+    mat = experimentplustheory_normcovmat(procs_covmat,
                                            theory_block_diag_covmat,
-                                           groups_data_values)
+                                           procs_data_values)
     return mat
 
 @table
-def experimentplustheory_normcovmat_custom(groups_covmat,
+def experimentplustheory_normcovmat_custom(procs_covmat,
                                             theory_covmat_custom,
-                                            groups_data_values,
+                                            procs_data_values,
                                             experimentplustheory_normcovmat):
     """Calculates the experiment + theory covariance matrix for scale
        variations normalised to data, correlations by process type."""
-    mat = experimentplustheory_normcovmat(groups_covmat,
+    mat = experimentplustheory_normcovmat(procs_covmat,
                                            theory_covmat_custom,
-                                           groups_data_values)
+                                           procs_data_values)
 
     return mat
 @table
-def experimentplustheory_corrmat_singleprocess(groups_covmat,
+def experimentplustheory_corrmat_singleprocess(procs_covmat,
                                                 theory_covmat_singleprocess):
     """Calculates the correlation matrix for the experimental
     plus theory covariance matrices."""
-    total_df = groups_covmat + theory_covmat_singleprocess
-    total_cov = (groups_covmat + theory_covmat_singleprocess).values
+    total_df = procs_covmat + theory_covmat_singleprocess
+    total_cov = (procs_covmat + theory_covmat_singleprocess).values
     diag_minus_half = (np.diagonal(total_cov))**(-0.5)
     corrmat = diag_minus_half[:,np.newaxis]*total_df*diag_minus_half
     return corrmat
 
 @table
-def experimentplusblocktheory_corrmat(groups_covmat,
+def experimentplusblocktheory_corrmat(procs_covmat,
                                        theory_block_diag_covmat):
     """Calculates the correlation matrix for the experimental
     plus theory covariance matrices, block diagonal by dataset."""
-    corrmat = experimentplustheory_corrmat_singleprocess(groups_covmat,
+    corrmat = experimentplustheory_corrmat_singleprocess(procs_covmat,
                                             theory_block_diag_covmat)
     return corrmat
 
 @table
-def experimentplustheory_corrmat_custom(groups_covmat,
+def experimentplustheory_corrmat_custom(procs_covmat,
                                          theory_covmat_custom):
     """Calculates the correlation matrix for the experimental
     plus theory covariance matrices, correlations by prescription."""
-    corrmat = experimentplustheory_corrmat_singleprocess(groups_covmat,
+    corrmat = experimentplustheory_corrmat_singleprocess(procs_covmat,
                                             theory_covmat_custom)
     return corrmat
 
-def chi2_impact(theory_covmat_singleprocess, groups_covmat, groups_results):
+def chi2_impact(theory_covmat_singleprocess, procs_covmat, procs_results):
     """Returns total chi2 including theory cov mat"""
-    dataresults, theoryresults = zip(*groups_results)
+    dataresults, theoryresults = zip(*procs_results)
     dat_central_list = [x.central_value for x in dataresults]
     th_central_list = [x.central_value for x in theoryresults]
     dat_central = np.concatenate(dat_central_list)
     th_central  = np.concatenate([x for x in th_central_list])
     central_diff = dat_central - th_central
-    cov = theory_covmat_singleprocess.values + groups_covmat.values
+    cov = theory_covmat_singleprocess.values + procs_covmat.values
     return calc_chi2(la.cholesky(cov, lower=True), central_diff)/len(central_diff)
 
-def data_theory_diff(groups_results):
+def data_theory_diff(procs_results):
     """Returns (D-T) for central theory, for use in chi2 calculations"""
-    dataresults, theoryresults = zip(*groups_results)
+    dataresults, theoryresults = zip(*procs_results)
     dat_central_list = [x.central_value for x in dataresults]
     th_central_list = [x.central_value for x in theoryresults]
     dat_central = np.concatenate(dat_central_list)
@@ -555,19 +555,19 @@ def data_theory_diff(groups_results):
     central_diff = dat_central - th_central
     return central_diff
 
-def chi2_block_impact(theory_block_diag_covmat, groups_covmat,
-                      groups_results):
+def chi2_block_impact(theory_block_diag_covmat, procs_covmat,
+                      procs_results):
     """Returns total chi2 including theory cov mat"""
-    chi2 = chi2_impact(theory_block_diag_covmat, groups_covmat,
-                       groups_results)
+    chi2 = chi2_impact(theory_block_diag_covmat, procs_covmat,
+                       procs_results)
     return chi2
 
 
-def chi2_impact_custom(theory_covmat_custom, groups_covmat,
-                       groups_results):
+def chi2_impact_custom(theory_covmat_custom, procs_covmat,
+                       procs_results):
     """Returns total chi2 including theory cov mat"""
-    chi2 = chi2_impact(theory_covmat_custom, groups_covmat,
-                       groups_results)
+    chi2 = chi2_impact(theory_covmat_custom, procs_covmat,
+                       procs_results)
     return chi2
 
 def theory_diagcovmat(theory_covmat_singleprocess):
@@ -578,14 +578,14 @@ def theory_diagcovmat(theory_covmat_singleprocess):
     np.fill_diagonal(s_diag, np.diag(s))
     return s_diag
 
-def chi2_diag_only(theory_diagcovmat, groups_covmat, data_theory_diff):
+def chi2_diag_only(theory_diagcovmat, procs_covmat, data_theory_diff):
     """Returns total chi2 including only diags of theory cov mat"""
-    cov = theory_diagcovmat + groups_covmat.values
+    cov = theory_diagcovmat + procs_covmat.values
     elements = np.dot(data_theory_diff.T,np.dot(la.inv(cov),data_theory_diff))
     chi2 = (1/len(data_theory_diff))*np.sum(elements)
     return chi2
 
-each_dataset_results = collect(results, ('group_dataset_inputs_by_metadata', 'data'))
+each_dataset_results = collect(results, ('proc_dataset_inputs_by_metadata', 'data'))
 
 def abs_chi2_data_theory_dataset(each_dataset_results, total_covmat_datasets):
     """Returns an array of tuples (member_chi², central_chi², numpoints)
@@ -599,10 +599,10 @@ def abs_chi2_data_theory_dataset(each_dataset_results, total_covmat_datasets):
                                    central_result, len(data_result)))
     return chi2data_array
 
-def abs_chi2_data_theory_group(groups_results, total_covmat_groups):
-    """Like abs_chi2_data_theory_dataset but for groups not datasets"""
+def abs_chi2_data_theory_proc(procs_results, total_covmat_procs):
+    """Like abs_chi2_data_theory_dataset but for procs not datasets"""
     chi2data_array = []
-    for expresults, covmat in zip(groups_results, total_covmat_groups):
+    for expresults, covmat in zip(procs_results, total_covmat_procs):
         data_result, th_result = expresults
         chi2s = all_chi2_theory(expresults, covmat)
         central_result = central_chi2_theory(expresults, covmat)
@@ -610,11 +610,11 @@ def abs_chi2_data_theory_group(groups_results, total_covmat_groups):
                               central_result, len(data_result)))
     return chi2data_array
 
-def abs_chi2_data_diagtheory_group(groups_results,
-                                        total_covmat_diagtheory_groups):
+def abs_chi2_data_diagtheory_proc(procs_results,
+                                        total_covmat_diagtheory_procs):
     """For a diagonal theory covmat"""
-    return abs_chi2_data_theory_group(groups_results,
-                                           total_covmat_diagtheory_groups)
+    return abs_chi2_data_theory_proc(procs_results,
+                                           total_covmat_diagtheory_procs)
 
 def abs_chi2_data_diagtheory_dataset(each_dataset_results,
                                      total_covmat_diagtheory_datasets):
diff --git a/validphys2/src/validphys/theorycovariance/output.py b/validphys2/src/validphys/theorycovariance/output.py
index fc0f855210..80511adc5f 100644
--- a/validphys2/src/validphys/theorycovariance/output.py
+++ b/validphys2/src/validphys/theorycovariance/output.py
@@ -18,31 +18,31 @@
 from reportengine.table import table
 
 from validphys import plotutils
-from validphys.results import groups_chi2_table
+from validphys.results import procs_chi2_table
 
 log = logging.getLogger(__name__)
 
 
 @table
-def groups_chi2_table_theory(
-    groups_data, pdf, abs_chi2_data_theory_group, abs_chi2_data_theory_dataset
+def procs_chi2_table_theory(
+    procs_data, pdf, abs_chi2_data_theory_proc, abs_chi2_data_theory_dataset
 ):
-    """Same as groups_chi2_table but including theory covariance matrix"""
-    return groups_chi2_table(
-        groups_data, pdf, abs_chi2_data_theory_group, abs_chi2_data_theory_dataset
+    """Same as procs_chi2_table but including theory covariance matrix"""
+    return procs_chi2_table(
+        procs_data, pdf, abs_chi2_data_theory_proc, abs_chi2_data_theory_dataset
     )
 
 
 @table
-def groups_chi2_table_diagtheory(
-    groups_data, pdf, abs_chi2_data_diagtheory_group, abs_chi2_data_diagtheory_dataset
+def procs_chi2_table_diagtheory(
+    procs_data, pdf, abs_chi2_data_diagtheory_proc, abs_chi2_data_diagtheory_dataset
 ):
-    """Same as groups_chi2_table but including
+    """Same as procs_chi2_table but including
     diagonal theory covariance matrix"""
-    return groups_chi2_table(
-        groups_data,
+    return procs_chi2_table(
+        procs_data,
         pdf,
-        abs_chi2_data_diagtheory_group,
+        abs_chi2_data_diagtheory_proc,
         abs_chi2_data_diagtheory_dataset,
     )
 
@@ -210,19 +210,19 @@ def plot_corrmat_heatmap(corrmat, title):
 
 
 @figure
-def plot_normexpcovmat_heatmap(groups_normcovmat):
+def plot_normexpcovmat_heatmap(procs_normcovmat):
     """Matrix plot of the experiment covariance matrix normalised to data."""
     fig = plot_covmat_heatmap(
-        groups_normcovmat, "Experimental Covariance Matrix"
+        procs_normcovmat, "Experimental Covariance Matrix"
     )
     return fig
 
 
 @figure
-def plot_expcorrmat_heatmap(groups_corrmat):
+def plot_expcorrmat_heatmap(procs_corrmat):
     """Matrix plot of the experiment correlation matrix"""
     fig = plot_corrmat_heatmap(
-        groups_corrmat, "Experimental Correlation Matrix"
+        procs_corrmat, "Experimental Correlation Matrix"
     )
     return fig
 
@@ -347,10 +347,10 @@ def plot_expplusthcorrmat_heatmap_custom(
 
 
 @figure
-def plot_blockcovdiff_heatmap(theory_block_diag_covmat, groups_covmat):
+def plot_blockcovdiff_heatmap(theory_block_diag_covmat, procs_covmat):
     """Matrix plot (thcov + expcov)/expcov"""
-    df = (theory_block_diag_covmat.as_matrix() + groups_covmat.values) / np.mean(
-        groups_covmat.values
+    df = (theory_block_diag_covmat.as_matrix() + procs_covmat.values) / np.mean(
+        procs_covmat.values
     )
     fig = plot_covmat_heatmap(
         df,
@@ -363,7 +363,7 @@ def plot_blockcovdiff_heatmap(theory_block_diag_covmat, groups_covmat):
 @figure
 def plot_covdiff_heatmap_custom(
     theory_covmat_custom,
-    groups_covmat,
+    procs_covmat,
     theoryids,
     fivetheories: (str, type(None)) = None,
 ):
@@ -374,7 +374,7 @@ def plot_covdiff_heatmap_custom(
             l = r"$\bar{5}$"
         elif fivetheories == "linear":
             l = "linear 5"
-    df = (theory_covmat_custom + groups_covmat) / np.mean(groups_covmat.values)
+    df = (theory_covmat_custom + procs_covmat) / np.mean(procs_covmat.values)
     fig = plot_covmat_heatmap(
         df,
         "(Theory + experiment)/mean(experiment)"
@@ -386,8 +386,8 @@ def plot_covdiff_heatmap_custom(
 @figure
 def plot_diag_cov_comparison(
     theory_covmat_custom,
-    groups_covmat,
-    groups_data_values,
+    procs_covmat,
+    procs_data_values,
     theoryids,
     fivetheories: (str, type(None)) = None,
 ):
@@ -398,7 +398,7 @@ def plot_diag_cov_comparison(
             l = r"$\bar{5}$"
         elif fivetheories == "linear":
             l = "linear 5"
-    data = np.abs(groups_data_values)
+    data = np.abs(procs_data_values)
     plot_index = theory_covmat_custom.index
     sqrtdiags_th = np.sqrt(np.diag(theory_covmat_custom)) / data
     sqrtdiags_th = pd.DataFrame(sqrtdiags_th.values, index=plot_index)
@@ -406,11 +406,11 @@ def plot_diag_cov_comparison(
     oldindex = sqrtdiags_th.index.tolist()
     newindex = sorted(oldindex, key=_get_key)
     sqrtdiags_th = sqrtdiags_th.reindex(newindex)
-    sqrtdiags_exp = np.sqrt(np.diag(groups_covmat)) / data
+    sqrtdiags_exp = np.sqrt(np.diag(procs_covmat)) / data
     sqrtdiags_exp = pd.DataFrame(sqrtdiags_exp.values, index=plot_index)
     sqrtdiags_exp.sort_index(0, inplace=True)
     sqrtdiags_exp = sqrtdiags_exp.reindex(newindex)
-    df_total = theory_covmat_custom + groups_covmat
+    df_total = theory_covmat_custom + procs_covmat
     sqrtdiags_tot = np.sqrt(np.diag(df_total)) / data
     sqrtdiags_tot = pd.DataFrame(sqrtdiags_tot.values, index=plot_index)
     sqrtdiags_tot.sort_index(0, inplace=True)
@@ -440,8 +440,8 @@ def plot_diag_cov_comparison(
 @figure
 def plot_diag_cov_impact(
     theory_covmat_custom,
-    groups_covmat,
-    groups_data_values,
+    procs_covmat,
+    procs_data_values,
     theoryids,
     fivetheories: (str, type(None)) = None,
 ):
@@ -453,11 +453,11 @@ def plot_diag_cov_impact(
         elif fivetheories == "linear":
             l = "linear 5"
     matrix_theory = theory_covmat_custom.values
-    matrix_experiment = groups_covmat.values
-    inv_exp = (np.diag(la.inv(matrix_experiment))) ** (-0.5) / groups_data_values
+    matrix_experiment = procs_covmat.values
+    inv_exp = (np.diag(la.inv(matrix_experiment))) ** (-0.5) / procs_data_values
     inv_tot = (np.diag(la.inv(matrix_theory + matrix_experiment))) ** (
         -0.5
-    ) / groups_data_values
+    ) / procs_data_values
     plot_index = theory_covmat_custom.index
     df_inv_exp = pd.DataFrame(inv_exp, index=plot_index)
     df_inv_exp.sort_index(0, inplace=True)
@@ -486,7 +486,7 @@ def plot_diag_cov_impact(
 
 @figure
 def plot_datasets_chi2_theory(
-    groups_data, each_dataset_chi2, abs_chi2_data_theory_dataset
+    procs_data, each_dataset_chi2, abs_chi2_data_theory_dataset
 ):
     """Plot the chi² of all datasets, before and after adding theory errors, with bars."""
     ds = iter(each_dataset_chi2)
@@ -494,12 +494,12 @@ def plot_datasets_chi2_theory(
     dschi2 = []
     dschi2theory = []
     xticks = []
-    for group in groups_data:
-        for dataset, dsres in zip(group, ds):
+    for proc in procs_data:
+        for dataset, dsres in zip(proc, ds):
             dschi2.append(dsres.central_result / dsres.ndata)
             xticks.append(dataset.name)
-    for group in groups_data:
-        for dataset, dsres in zip(group, dstheory):
+    for proc in procs_data:
+        for dataset, dsres in zip(proc, dstheory):
             dschi2theory.append(dsres.central_result / dsres.ndata)
     plotvalues = np.stack((dschi2theory, dschi2))
     fig, ax = plotutils.barplot(

From ce0404090421b21f12172596f74d1da59bfe634f Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 11:04:43 +0000
Subject: [PATCH 06/11] fix bugs

---
 validphys2/src/validphys/results.py                 |  4 ++--
 .../src/validphys/theorycovariance/construction.py  |  2 +-
 validphys2/src/validphys/theorycovariance/output.py | 13 +++++++------
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/validphys2/src/validphys/results.py b/validphys2/src/validphys/results.py
index 88028a7ec7..609e9c7c49 100644
--- a/validphys2/src/validphys/results.py
+++ b/validphys2/src/validphys/results.py
@@ -1285,12 +1285,12 @@ def groups_central_values(group_result_table):
     central_theory_values = group_result_table["theory_central"]
     return central_theory_values
 
-def procs_central_values_no_table(proc_result_table):
+def procs_central_values_no_table(proc_result_table_no_table):
     central_theory_values = proc_result_table_no_table["theory_central"]
     return central_theory_values
 
 @table
-def procs_central_values(proc_result_table):
+def procs_central_values(procs_central_values_no_table):
     return procs_central_values_no_table
 
 dataspecs_each_dataset_chi2 = collect("each_dataset_chi2", ("dataspecs",))
diff --git a/validphys2/src/validphys/theorycovariance/construction.py b/validphys2/src/validphys/theorycovariance/construction.py
index 65c8c30a82..8f6e248282 100644
--- a/validphys2/src/validphys/theorycovariance/construction.py
+++ b/validphys2/src/validphys/theorycovariance/construction.py
@@ -585,7 +585,7 @@ def chi2_diag_only(theory_diagcovmat, procs_covmat, data_theory_diff):
     chi2 = (1/len(data_theory_diff))*np.sum(elements)
     return chi2
 
-each_dataset_results = collect(results, ('proc_dataset_inputs_by_metadata', 'data'))
+each_dataset_results = collect(results, ('force_process_grouping', 'data'))
 
 def abs_chi2_data_theory_dataset(each_dataset_results, total_covmat_datasets):
     """Returns an array of tuples (member_chi², central_chi², numpoints)
diff --git a/validphys2/src/validphys/theorycovariance/output.py b/validphys2/src/validphys/theorycovariance/output.py
index 80511adc5f..4610678a89 100644
--- a/validphys2/src/validphys/theorycovariance/output.py
+++ b/validphys2/src/validphys/theorycovariance/output.py
@@ -18,7 +18,7 @@
 from reportengine.table import table
 
 from validphys import plotutils
-from validphys.results import procs_chi2_table
+from validphys.results import groups_chi2_table
 
 log = logging.getLogger(__name__)
 
@@ -27,8 +27,9 @@
 def procs_chi2_table_theory(
     procs_data, pdf, abs_chi2_data_theory_proc, abs_chi2_data_theory_dataset
 ):
-    """Same as procs_chi2_table but including theory covariance matrix"""
-    return procs_chi2_table(
+    """Same as groups_chi2_table but including theory covariance matrix.
+    Note: we use groups_chi2_table here but provide data grouped by process."""
+    return groups_chi2_table(
         procs_data, pdf, abs_chi2_data_theory_proc, abs_chi2_data_theory_dataset
     )
 
@@ -37,9 +38,9 @@ def procs_chi2_table_theory(
 def procs_chi2_table_diagtheory(
     procs_data, pdf, abs_chi2_data_diagtheory_proc, abs_chi2_data_diagtheory_dataset
 ):
-    """Same as procs_chi2_table but including
-    diagonal theory covariance matrix"""
-    return procs_chi2_table(
+    """Same as groups_chi2_table but including diagonal theory covariance matrix.
+    Note: we use groups_chi2_table here but provide data grouped by process."""
+    return groups_chi2_table(
         procs_data,
         pdf,
         abs_chi2_data_diagtheory_proc,

From e556fee9a29ee918bf50f7b27462682d526749cd Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 11:13:09 +0000
Subject: [PATCH 07/11] update action name in template

---
 .../examples/theory_covariance/template_matrix_plots.md       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/validphys2/examples/theory_covariance/template_matrix_plots.md b/validphys2/examples/theory_covariance/template_matrix_plots.md
index 671074e3e7..8e200fb46f 100644
--- a/validphys2/examples/theory_covariance/template_matrix_plots.md
+++ b/validphys2/examples/theory_covariance/template_matrix_plots.md
@@ -30,11 +30,11 @@ Total (exp. + th.) $\chi^2$
 
 Experimental $\chi^2$ by dataset
 --------------------------------
-   {@groups_chi2_table@}
+   {@procs_chi2_table@}
 
 Total (exp. + th.) $\chi^2$ by dataset
 --------------------------------------
-   {@groups_chi2_table_theory@}
+   {@procs_chi2_table_theory@}
 
 $\chi^2$ including only diagonal theory elements
 ------------------------------------------------

From 083b49150c41774d753b92d0a04ed9365e5feae3 Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 11:14:33 +0000
Subject: [PATCH 08/11] remove metadata_process in runcard

---
 .../examples/theory_covariance/covariance_matrix_plots.yaml     | 2 --
 1 file changed, 2 deletions(-)

diff --git a/validphys2/examples/theory_covariance/covariance_matrix_plots.yaml b/validphys2/examples/theory_covariance/covariance_matrix_plots.yaml
index 772d95c2f4..fe5f32b32d 100644
--- a/validphys2/examples/theory_covariance/covariance_matrix_plots.yaml
+++ b/validphys2/examples/theory_covariance/covariance_matrix_plots.yaml
@@ -3,8 +3,6 @@ meta:
    keywords: [theory uncertainties, 3-point]
    title: NLO 3-point variations for 5 process types - DIS CC, DIS NC, DY, Top, Jets
 
-metadata_group: nnpdf31_process
-
 default_theory:
    - theoryid: 163
 

From 5da329e5a865cd5e18ed1e0c15ea846d0ceee712 Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Tue, 9 Mar 2021 11:26:35 +0000
Subject: [PATCH 09/11] fix proc table

---
 validphys2/src/validphys/results.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/validphys2/src/validphys/results.py b/validphys2/src/validphys/results.py
index 609e9c7c49..6b753ad8dd 100644
--- a/validphys2/src/validphys/results.py
+++ b/validphys2/src/validphys/results.py
@@ -827,14 +827,14 @@ def groups_chi2_table(groups_data, pdf, groups_chi2, each_dataset_chi2):
     return pd.DataFrame(records)
 
 
+@table
+def procs_chi2_table(procs_data, pdf, procs_chi2, each_dataset_chi2):
+    return groups_chi2_table(procs_data, pdf, procs_chi2, each_dataset_chi2)
+    
 experiments_chi2_table = collect(
     "groups_chi2_table", ("group_dataset_inputs_by_experiment",)
 )
 
-procs_chi2_table = collect(
-    "groups_chi2_table", ("force_process_grouping",)
-)
-
 @check_cuts_considered
 @table
 def closure_shifts(experiments_index, fit, use_cuts, experiments):
@@ -953,6 +953,9 @@ def dataset_chi2_table(chi2_stats, dataset):
     "dataset_inputs_abs_chi2_data", ("group_dataset_inputs_by_metadata",)
 )
 
+procs_chi2 = collect("dataset_inputs_abs_chi2_data", ("force_process_grouping",)
+)
+
 fits_groups_chi2_data = collect("groups_chi2", ("fits", "fitcontext"))
 fits_groups = collect("groups_data", ("fits", "fitcontext",))
 

From cee2829783831ae49a493ee31de8240406ed5a6c Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Wed, 10 Mar 2021 10:38:50 +0000
Subject: [PATCH 10/11] change name  to by_process

---
 validphys2/src/validphys/config.py                        | 2 +-
 validphys2/src/validphys/results.py                       | 6 +++---
 validphys2/src/validphys/theorycovariance/construction.py | 6 +++---
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/validphys2/src/validphys/config.py b/validphys2/src/validphys/config.py
index 56598fcd5c..0db766e5d3 100644
--- a/validphys2/src/validphys/config.py
+++ b/validphys2/src/validphys/config.py
@@ -1358,7 +1358,7 @@ def produce_group_dataset_inputs_by_metadata(
     def produce_group_dataset_inputs_by_experiment(self, data_input):
         return self.produce_group_dataset_inputs_by_metadata(data_input, "experiment")
 
-    def produce_force_process_grouping(self, data_input):
+    def produce_group_dataset_inputs_by_process(self, data_input):
         return self.produce_group_dataset_inputs_by_metadata(data_input, "nnpdf31_process")
 
     def produce_scale_variation_theories(self, theoryid, point_prescription):
diff --git a/validphys2/src/validphys/results.py b/validphys2/src/validphys/results.py
index 6b753ad8dd..25121d689b 100644
--- a/validphys2/src/validphys/results.py
+++ b/validphys2/src/validphys/results.py
@@ -154,7 +154,7 @@ def rawdata(self):
 
 experiments_data = collect("data", ("group_dataset_inputs_by_experiment",))
 
-procs_data = collect("data", ("force_process_grouping",))
+procs_data = collect("data", ("group_dataset_inputs_by_process",))
 
 def groups_index(groups_data):
     """Return a pandas.MultiIndex with levels for group, dataset and point
@@ -212,7 +212,7 @@ def procs_data_values(proc_result_table):
 )
 
 procs_results = collect(
-    "dataset_inputs_results", ("force_process_grouping",)
+    "dataset_inputs_results", ("group_dataset_inputs_by_process",)
 )
 
 def group_result_table_no_table(groups_results, groups_index):
@@ -953,7 +953,7 @@ def dataset_chi2_table(chi2_stats, dataset):
     "dataset_inputs_abs_chi2_data", ("group_dataset_inputs_by_metadata",)
 )
 
-procs_chi2 = collect("dataset_inputs_abs_chi2_data", ("force_process_grouping",)
+procs_chi2 = collect("dataset_inputs_abs_chi2_data", ("group_dataset_inputs_by_process",)
 )
 
 fits_groups_chi2_data = collect("groups_chi2", ("fits", "fitcontext"))
diff --git a/validphys2/src/validphys/theorycovariance/construction.py b/validphys2/src/validphys/theorycovariance/construction.py
index 8f6e248282..a9ad01cfe7 100644
--- a/validphys2/src/validphys/theorycovariance/construction.py
+++ b/validphys2/src/validphys/theorycovariance/construction.py
@@ -70,7 +70,7 @@ def theory_covmat_singleprocess(theory_covmat_singleprocess_no_table,
 
 results_bytheoryids = collect(results,('theoryids',))
 each_dataset_results_bytheory = collect('results_bytheoryids',
-                                        ('force_process_grouping','data'))
+                                        ('group_dataset_inputs_by_process','data'))
 
 @check_correct_theory_combination
 def theory_covmat_datasets(each_dataset_results_bytheory,
@@ -151,7 +151,7 @@ def total_covmat_procs(procs_results_theory,
         proc_result_covmats.append(cov)
     return proc_result_covmats
 
-commondata_procs = collect('commondata', ['force_process_grouping', 'data'])
+commondata_procs = collect('commondata', ['group_dataset_inputs_by_process', 'data'])
 
 def dataset_names(commondata_procs):
     """Returns a list of the names of the datasets, in the same order as
@@ -585,7 +585,7 @@ def chi2_diag_only(theory_diagcovmat, procs_covmat, data_theory_diff):
     chi2 = (1/len(data_theory_diff))*np.sum(elements)
     return chi2
 
-each_dataset_results = collect(results, ('force_process_grouping', 'data'))
+each_dataset_results = collect(results, ('group_dataset_inputs_by_process', 'data'))
 
 def abs_chi2_data_theory_dataset(each_dataset_results, total_covmat_datasets):
     """Returns an array of tuples (member_chi², central_chi², numpoints)

From fd84f50db0bb04d4c774bacb182379e9d98deaee Mon Sep 17 00:00:00 2001
From: RosalynLP <rosalynlaurap@gmail.com>
Date: Wed, 10 Mar 2021 10:40:27 +0000
Subject: [PATCH 11/11] review comments

---
 validphys2/src/validphys/theorycovariance/construction.py | 4 ++--
 validphys2/src/validphys/theorycovariance/output.py       | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/validphys2/src/validphys/theorycovariance/construction.py b/validphys2/src/validphys/theorycovariance/construction.py
index a9ad01cfe7..b2636c52d1 100644
--- a/validphys2/src/validphys/theorycovariance/construction.py
+++ b/validphys2/src/validphys/theorycovariance/construction.py
@@ -52,8 +52,8 @@ def make_scale_var_covmat(predictions):
 
 @check_correct_theory_combination
 def theory_covmat_singleprocess_no_table(theoryids_procs_central_values_no_table,
-                           procs_index, theoryids,
-                           fivetheories:(str, type(None)) = None):
+                                         procs_index, theoryids,
+                                         fivetheories:(str, type(None)) = None):
 
     """Calculates the theory covariance matrix for scale variations.
     The matrix is a dataframe indexed by procs_index."""
diff --git a/validphys2/src/validphys/theorycovariance/output.py b/validphys2/src/validphys/theorycovariance/output.py
index 4610678a89..b2765febac 100644
--- a/validphys2/src/validphys/theorycovariance/output.py
+++ b/validphys2/src/validphys/theorycovariance/output.py
@@ -180,7 +180,6 @@ def _get_key(element):
     return newelement
 
 
-@figure
 def plot_corrmat_heatmap(corrmat, title):
     """Matrix plot of a correlation matrix"""
     df = corrmat