chore: Renamed src namespaces and path from iql to gensql

Retained old inferenceql symbols in gpm/readers, for backwards-compatibility.

README.md

@@ -1,4 +1,4 @@
-# inferenceql.inference
+# GenSQL.inference
 
-![tests](https://github.com/probcomp/inferenceql.inference/workflows/tests/badge.svg)
-![linter](https://github.com/probcomp/inferenceql.inference/workflows/lint/badge.svg)
+![tests](https://github.com/OpenGen/GenSQL.inference/workflows/tests/badge.svg)
+![linter](https://github.com/OpenGen/GenSQL.inference/workflows/lint/badge.svg)

src/inferenceql/inference/approximate.cljc → src/gensql/inference/approximate.cljc

@@ -1,6 +1,6 @@
-(ns inferenceql.inference.approximate
-  (:require [inferenceql.inference.gpm.proto :as gpm.proto]
-            [inferenceql.inference.utils :as utils]))
+(ns gensql.inference.approximate
+  (:require [gensql.inference.gpm.proto :as gpm.proto]
+            [gensql.inference.utils :as utils]))
 
 (defn mutual-info
   "Given a GPM, estimates the mutual-information of `target-a` and `target-b`

src/inferenceql/inference/distributions.cljc → src/gensql/inference/distributions.cljc

@@ -1,7 +1,7 @@
-(ns inferenceql.inference.distributions
+(ns gensql.inference.distributions
   (:require [clojure.math :as math]
             [clojure.spec.alpha :as s]
-            [inferenceql.inference.gpm.multimixture.specification :as spec]
+            [gensql.inference.gpm.multimixture.specification :as spec]
             [metaprob.distributions]
             [metaprob.prelude :as mp]))
 

src/inferenceql/inference/dpm.cljc → src/gensql/inference/dpm.cljc

@@ -1,4 +1,4 @@
-(ns inferenceql.inference.dpm
+(ns gensql.inference.dpm
   "Functions operating on discriminative population models. All probabilistic
   models for which you can simulate and compute the log-PDF only for a set of
   dependent variables (most typically 1 column variable), and for which
@@ -40,8 +40,8 @@
                      :dpm dpm}))))
 
 (defn assert-args-valid
-  "Asserts that `inferenceql.inference.gpm/logpdf` and
-  `inferenceql.inference.gpm/constraints` can be called with the provided
+  "Asserts that `gensql.inference.gpm/logpdf` and
+  `gensql.inference.gpm/constraints` can be called with the provided
   targeted and constrained variables."
   [dpm target-variables constrained-variables]
   (assert-targets-dependent dpm target-variables)

src/inferenceql/inference/event.cljc → src/gensql/inference/event.cljc

@@ -1,4 +1,4 @@
-(ns inferenceql.inference.event
+(ns gensql.inference.event
   "Functions to process SPPL-style events.")
 
 (defn operator

src/inferenceql/inference/gpm.cljc → src/gensql/inference/gpm.cljc

@@ -1,19 +1,19 @@
-(ns inferenceql.inference.gpm
+(ns gensql.inference.gpm
   (:refer-clojure :exclude [merge read read-string])
   (:require [clojure.core :as clojure]
             [clojure.edn :as edn]
-            [inferenceql.inference.gpm.column :as column]
-            [inferenceql.inference.gpm.compositional :as compositional]
-            [inferenceql.inference.gpm.crosscat :as xcat]
-            #?(:clj [inferenceql.inference.gpm.ensemble :as ensemble])
-            #?(:clj [inferenceql.inference.gpm.http :as http])
-            [inferenceql.inference.gpm.multimixture :as mmix]
-            [inferenceql.inference.gpm.multimixture.specification :as mmix.spec]
-            [inferenceql.inference.gpm.primitive-gpms.bernoulli :as bernoulli]
-            [inferenceql.inference.gpm.primitive-gpms.categorical :as categorical]
-            [inferenceql.inference.gpm.primitive-gpms.gaussian :as gaussian]
-            [inferenceql.inference.gpm.proto :as gpm-proto]
-            [inferenceql.inference.gpm.view :as view]))
+            [gensql.inference.gpm.column :as column]
+            [gensql.inference.gpm.compositional :as compositional]
+            [gensql.inference.gpm.crosscat :as xcat]
+            #?(:clj [gensql.inference.gpm.ensemble :as ensemble])
+            #?(:clj [gensql.inference.gpm.http :as http])
+            [gensql.inference.gpm.multimixture :as mmix]
+            [gensql.inference.gpm.multimixture.specification :as mmix.spec]
+            [gensql.inference.gpm.primitive-gpms.bernoulli :as bernoulli]
+            [gensql.inference.gpm.primitive-gpms.categorical :as categorical]
+            [gensql.inference.gpm.primitive-gpms.gaussian :as gaussian]
+            [gensql.inference.gpm.proto :as gpm-proto]
+            [gensql.inference.gpm.view :as view]))
 
 #?(:clj
    (defn http
@@ -144,7 +144,18 @@
   (gpm-proto/constrain gpm event opts))
 
 (def readers
-  {'inferenceql.inference.gpm.column.Column column/map->Column
+  {'gensql.inference.gpm.column.Column column/map->Column
+   'gensql.inference.gpm.compositional.Compositional compositional/map->Compositional
+   'gensql.inference.gpm.crosscat.XCat xcat/map->XCat
+   #?@(:clj ['gensql.inference.gpm.ensemble.Ensemble ensemble/map->Ensemble])
+   'gensql.inference.gpm.multimixture.Multimixture mmix/map->Multimixture
+   'gensql.inference.gpm.primitive_gpms.bernoulli.Bernoulli bernoulli/map->Bernoulli
+   'gensql.inference.gpm.primitive_gpms.categorical.Categorical categorical/map->Categorical
+   'gensql.inference.gpm.primitive_gpms.gaussian.Gaussian gaussian/map->Gaussian
+   'gensql.inference.gpm.view.View view/map->View
+
+   ;; for backwards-compatibility with older models
+   'inferenceql.inference.gpm.column.Column column/map->Column
    'inferenceql.inference.gpm.compositional.Compositional compositional/map->Compositional
    'inferenceql.inference.gpm.crosscat.XCat xcat/map->XCat
    #?@(:clj ['inferenceql.inference.gpm.ensemble.Ensemble ensemble/map->Ensemble])
@@ -166,7 +177,7 @@
 
 (defn read
   "Like `clojure.edn/read` but includes readers for records in
-  `inferneceql.inference`."
+  `gensql.inference`."
   ([stream]
    (read {} stream))
   ([opts stream]
@@ -176,7 +187,7 @@
 
 (defn ^:export read-string
   "Like `clojure.edn/read-string` but includes readers for records from
-  `inferenceql.inference`."
+  `gensql.inference`."
   ([s]
    (read-string {} s))
   ([opts s]

src/inferenceql/inference/gpm/column.cljc → src/gensql/inference/gpm/column.cljc

@@ -1,14 +1,14 @@
-(ns inferenceql.inference.gpm.column
+(ns gensql.inference.gpm.column
   "Implementation of a GPM that represents a population of data of the
   same primitive type. For a tabular dataset, this GPM abstracts a Column
-  of that dataset. See `inferenceql.inference.gpm/column` for details."
+  of that dataset. See `gensql.inference.gpm/column` for details."
   (:require [clojure.math :as math]
-            [inferenceql.inference.gpm.conditioned :as conditioned]
-            [inferenceql.inference.gpm.constrained :as constrained]
-            [inferenceql.inference.gpm.primitive-gpms :as pgpms]
-            [inferenceql.inference.gpm.proto :as gpm.proto]
-            [inferenceql.inference.primitives :as primitives]
-            [inferenceql.inference.utils :as utils]))
+            [gensql.inference.gpm.conditioned :as conditioned]
+            [gensql.inference.gpm.constrained :as constrained]
+            [gensql.inference.gpm.primitive-gpms :as pgpms]
+            [gensql.inference.gpm.proto :as gpm.proto]
+            [gensql.inference.primitives :as primitives]
+            [gensql.inference.utils :as utils]))
 
 (defn crp-weights
   "Given a column and alpha, returns the CRP prior over categories."

src/inferenceql/inference/gpm/compositional.cljc → src/gensql/inference/gpm/compositional.cljc

@@ -1,7 +1,7 @@
-(ns inferenceql.inference.gpm.compositional
+(ns gensql.inference.gpm.compositional
   (:require [clojure.set :as set]
-            [inferenceql.inference.dpm :as dpm]
-            [inferenceql.inference.gpm.proto :as proto]
+            [gensql.inference.dpm :as dpm]
+            [gensql.inference.gpm.proto :as proto]
             [metaprob.distributions :as dist]))
 
 (defn ^:private monte-carlo-integration
@@ -26,7 +26,7 @@
           independent-targets (set/intersection target-variables independent-variables)]
       (cond (and (seq dependent-targets)
                  (seq independent-targets))
-            (throw (ex-info "`inferenceql.inference.gpm/logpdf` cannot be computed for a mixture of dependent and independent target variables."
+            (throw (ex-info "`gensql.inference.gpm/logpdf` cannot be computed for a mixture of dependent and independent target variables."
                             {:dependent-targets dependent-targets
                              :independent-targets independent-targets
                              :dpm dpm}))

src/inferenceql/inference/gpm/conditioned.cljc → src/gensql/inference/gpm/conditioned.cljc

@@ -1,5 +1,5 @@
-(ns inferenceql.inference.gpm.conditioned
-  (:require [inferenceql.inference.gpm.proto :as gpm.proto]))
+(ns gensql.inference.gpm.conditioned
+  (:require [gensql.inference.gpm.proto :as gpm.proto]))
 
 (defrecord ConditionedGPM [gpm conditions]
   gpm.proto/GPM
@@ -23,7 +23,7 @@
 
 (defn condition
   "Conditions gpm based on conditions via rejection sampling. Arguments are the
-  same as those for `inferenceql.inference.gom/condition`."
+  same as those for `gensql.inference.gom/condition`."
   [gpm conditions]
   (assert map? conditions)
   (->ConditionedGPM gpm conditions))

src/inferenceql/inference/gpm/constrained.cljc → src/gensql/inference/gpm/constrained.cljc

@@ -1,7 +1,7 @@
-(ns inferenceql.inference.gpm.constrained
+(ns gensql.inference.gpm.constrained
   (:refer-clojure :exclude [eval])
   (:require [clojure.math :as math]
-            [inferenceql.inference.gpm.proto :as gpm.proto]
+            [gensql.inference.gpm.proto :as gpm.proto]
             [net.cgrand.xforms.rfs :as rfs]))
 
 (defn ^:private and-f
@@ -78,7 +78,7 @@
 
 (defn constrain
   "Constrains gpm based on event via rejection sampling. Arguments are the same
-  as those for `inferenceql.inference.gpm/constrain`."
+  as those for `gensql.inference.gpm/constrain`."
   [gpm event opts]
   (let [pred? (event->pred event opts)
         variables (event->variables event opts)]

src/inferenceql/inference/gpm/crosscat.cljc → src/gensql/inference/gpm/crosscat.cljc

@@ -1,13 +1,13 @@
-(ns inferenceql.inference.gpm.crosscat
+(ns gensql.inference.gpm.crosscat
   (:require [clojure.set :as set]
             [clojure.edn :as edn]
-            [inferenceql.inference.gpm.conditioned :as conditioned]
-            [inferenceql.inference.gpm.constrained :as constrained]
-            [inferenceql.inference.gpm.view :as view]
-            [inferenceql.inference.gpm.column :as column]
-            [inferenceql.inference.gpm.primitive-gpms :as pgpms]
-            [inferenceql.inference.gpm.proto :as gpm.proto]
-            [inferenceql.inference.primitives :as primitives]))
+            [gensql.inference.gpm.conditioned :as conditioned]
+            [gensql.inference.gpm.constrained :as constrained]
+            [gensql.inference.gpm.view :as view]
+            [gensql.inference.gpm.column :as column]
+            [gensql.inference.gpm.primitive-gpms :as pgpms]
+            [gensql.inference.gpm.proto :as gpm.proto]
+            [gensql.inference.primitives :as primitives]))
 
 (defn update-hyper-grids
   "Given a collection of columns, updates the columns' respective hyper grids."

src/inferenceql/inference/gpm/ensemble.cljc → src/gensql/inference/gpm/ensemble.cljc

@@ -1,9 +1,9 @@
-(ns inferenceql.inference.gpm.ensemble
+(ns gensql.inference.gpm.ensemble
   (:require [clojure.math :as math]
-            [inferenceql.inference.gpm.conditioned :as conditioned]
-            [inferenceql.inference.gpm.constrained :as constrained]
-            [inferenceql.inference.gpm.proto :as gpm.proto]
-            [inferenceql.inference.utils :as utils])
+            [gensql.inference.gpm.conditioned :as conditioned]
+            [gensql.inference.gpm.constrained :as constrained]
+            [gensql.inference.gpm.proto :as gpm.proto]
+            [gensql.inference.utils :as utils])
   #?(:clj (:import [java.util ArrayList]
            [org.apache.commons.math3.distribution EnumeratedDistribution]
            [org.apache.commons.math3.util Pair])))

src/inferenceql/inference/gpm/http.clj → src/gensql/inference/gpm/http.clj

@@ -1,10 +1,10 @@
-(ns inferenceql.inference.gpm.http
+(ns gensql.inference.gpm.http
   "Implementation of a GPM that forwards requests over HTTP. See
-  `inferenceql.inference.gpm/http` for details."
+  `gensql.inference.gpm/http` for details."
   (:require [clj-http.client :as http]
-            [inferenceql.inference.gpm.conditioned :as conditioned]
-            [inferenceql.inference.gpm.constrained :as constrained]
-            [inferenceql.inference.gpm.proto :as proto]
+            [gensql.inference.gpm.conditioned :as conditioned]
+            [gensql.inference.gpm.constrained :as constrained]
+            [gensql.inference.gpm.proto :as proto]
             [jsonista.core :as json]))
 
 (defrecord HTTP [url]

src/inferenceql/inference/gpm/multimixture.cljc → src/gensql/inference/gpm/multimixture.cljc

@@ -1,9 +1,9 @@
-(ns inferenceql.inference.gpm.multimixture
+(ns gensql.inference.gpm.multimixture
   (:require [metaprob.prelude :as mp]
-            [inferenceql.inference.gpm.conditioned :as conditioned]
-            [inferenceql.inference.gpm.constrained :as constrained]
-            [inferenceql.inference.gpm.multimixture.utils :as mmix.utils]
-            [inferenceql.inference.gpm.proto :as gpm-proto]))
+            [gensql.inference.gpm.conditioned :as conditioned]
+            [gensql.inference.gpm.constrained :as constrained]
+            [gensql.inference.gpm.multimixture.utils :as mmix.utils]
+            [gensql.inference.gpm.proto :as gpm-proto]))
 
 ;; XXX Currently, assumes that the row generator of the mmix map is passed in.
 (defrecord Multimixture [vars views]

src/inferenceql/inference/gpm/multimixture/metrics.cljc → src/gensql/inference/gpm/multimixture/metrics.cljc

@@ -1,6 +1,6 @@
-(ns inferenceql.inference.gpm.multimixture.metrics
+(ns gensql.inference.gpm.multimixture.metrics
   (:require [clojure.math :as math]
-            [inferenceql.inference.gpm.multimixture.utils :as utils]))
+            [gensql.inference.gpm.multimixture.utils :as utils]))
 
 (defn check-distribution-criteria
   "Checks basic assumptions about two distributions being compared.
@@ -44,7 +44,7 @@
 (defn jensen-shannon-divergence
   "Calculates the Jenson-Shannon divergence between two distributions.
   Since it depends on
-  `inferenceql.inference.multimixture.metrics/kl-divergence`, `p` must be zero
+  `gensql.inference.multimixture.metrics/kl-divergence`, `p` must be zero
   when `q` is zero. `p` and `q` must have the same alphabet size (i.e. length)."
   [p q]
   (check-distribution-criteria p q)

src/inferenceql/inference/gpm/multimixture/metrics_viz.cljc → src/gensql/inference/gpm/multimixture/metrics_viz.cljc

@@ -1,6 +1,6 @@
-(ns inferenceql.inference.gpm.multimixture.metrics-viz
+(ns gensql.inference.gpm.multimixture.metrics-viz
   (:require [clojure.string :refer [split]]
-            [inferenceql.inference.gpm.multimixture.metrics :as metrics]))
+            [gensql.inference.gpm.multimixture.metrics :as metrics]))
 
 (defmacro with-out-str-data-time-map
   "Returns time and data of an expression of the form `(time expression)`

src/inferenceql/inference/gpm/multimixture/search.cljc → src/gensql/inference/gpm/multimixture/search.cljc

@@ -1,11 +1,11 @@
-(ns inferenceql.inference.gpm.multimixture.search
+(ns gensql.inference.gpm.multimixture.search
   (:require [clojure.math :as math]
             [clojure.spec.alpha :as s]
-            [inferenceql.inference.distributions :as idbdist]
-            [inferenceql.inference.gpm :as gpm]
-            [inferenceql.inference.gpm.multimixture.specification :as spec]
-            [inferenceql.inference.gpm.multimixture.utils :as mmix.utils]
-            [inferenceql.inference.utils :as utils]
+            [gensql.inference.distributions :as idbdist]
+            [gensql.inference.gpm :as gpm]
+            [gensql.inference.gpm.multimixture.specification :as spec]
+            [gensql.inference.gpm.multimixture.utils :as mmix.utils]
+            [gensql.inference.utils :as utils]
             [metaprob.distributions :as dist]
             [metaprob.generative-functions :as g :refer [at gen]]
             [metaprob.prelude :as mp]))

src/inferenceql/inference/gpm/multimixture/search/deterministic.cljc → src/gensql/inference/gpm/multimixture/search/deterministic.cljc

@@ -1,6 +1,6 @@
-(ns inferenceql.inference.gpm.multimixture.search.deterministic
-  (:require [inferenceql.inference.utils :as utils]
-            [inferenceql.inference.gpm.multimixture.search.utils :as search.utils]))
+(ns gensql.inference.gpm.multimixture.search.deterministic
+  (:require [gensql.inference.utils :as utils]
+            [gensql.inference.gpm.multimixture.search.utils :as search.utils]))
 
 #?(:cljs (enable-console-print!))
 

src/inferenceql/inference/gpm/multimixture/search/enumerative.cljc → src/gensql/inference/gpm/multimixture/search/enumerative.cljc

@@ -1,7 +1,7 @@
-(ns inferenceql.inference.gpm.multimixture.search.enumerative
+(ns gensql.inference.gpm.multimixture.search.enumerative
   (:require [clojure.math.combinatorics :as combo]
-            [inferenceql.inference.utils :as utils]
-            [inferenceql.inference.gpm.multimixture.search.utils :as search.utils]))
+            [gensql.inference.utils :as utils]
+            [gensql.inference.gpm.multimixture.search.utils :as search.utils]))
 
 (defn rows->all-cluster-configurations
   "Returns a (lazy) sequence of all possible cluster configurations for rows."

src/inferenceql/inference/gpm/multimixture/search/gibbs.cljc → src/gensql/inference/gpm/multimixture/search/gibbs.cljc

@@ -1,6 +1,6 @@
-(ns inferenceql.inference.gpm.multimixture.search.gibbs
+(ns gensql.inference.gpm.multimixture.search.gibbs
   (:require [metaprob.distributions :as dist]
-            [inferenceql.inference.gpm.multimixture.search.utils :as search.utils]))
+            [gensql.inference.gpm.multimixture.search.utils :as search.utils]))
 
 (defn sample-cluster-assignments
   "Given a probability table for rows, samples cluster assignments. A valid

src/inferenceql/inference/gpm/multimixture/search/utils.cljc → src/gensql/inference/gpm/multimixture/search/utils.cljc

@@ -1,6 +1,6 @@
-(ns inferenceql.inference.gpm.multimixture.search.utils
-  (:require [inferenceql.inference.gpm.multimixture.utils :as mmix.utils]
-            [inferenceql.inference.utils :as utils]
+(ns gensql.inference.gpm.multimixture.search.utils
+  (:require [gensql.inference.gpm.multimixture.utils :as mmix.utils]
+            [gensql.inference.utils :as utils]
             [metaprob.prelude :as mp]))
 
 (defn normalize-row-probability

src/inferenceql/inference/gpm/multimixture/specification.cljc → src/gensql/inference/gpm/multimixture/specification.cljc

@@ -1,4 +1,4 @@
-(ns inferenceql.inference.gpm.multimixture.specification
+(ns gensql.inference.gpm.multimixture.specification
   (:require [clojure.spec.alpha :as s]))
 
 (s/def ::alpha pos?)

src/inferenceql/inference/gpm/multimixture/utils.cljc → src/gensql/inference/gpm/multimixture/utils.cljc

@@ -1,12 +1,12 @@
-(ns inferenceql.inference.gpm.multimixture.utils
+(ns gensql.inference.gpm.multimixture.utils
   #?(:cljs (:require-macros [metaprob.generative-functions :refer [gen]]))
   (:require [clojure.math.combinatorics :as combo]
             [clojure.spec.alpha :as s]
             #?(:clj [metaprob.generative-functions :as g :refer [apply-at at gen]]
                :cljs [metaprob.generative-functions :as g :refer [apply-at at]])
             [metaprob.distributions :as dist]
             [metaprob.prelude :as mp]
-            [inferenceql.inference.gpm.multimixture.specification :as spec]))
+            [gensql.inference.gpm.multimixture.specification :as spec]))
 
 (defn row-generator
   "Returns a generative function that samples a row from the provided view

src/inferenceql/inference/gpm/primitive_gpms.cljc → src/gensql/inference/gpm/primitive_gpms.cljc

@@ -1,7 +1,7 @@
-(ns inferenceql.inference.gpm.primitive-gpms
-  (:require [inferenceql.inference.gpm.primitive-gpms.bernoulli :as bernoulli]
-            [inferenceql.inference.gpm.primitive-gpms.categorical :as categorical]
-            [inferenceql.inference.gpm.primitive-gpms.gaussian :as gaussian]))
+(ns gensql.inference.gpm.primitive-gpms
+  (:require [gensql.inference.gpm.primitive-gpms.bernoulli :as bernoulli]
+            [gensql.inference.gpm.primitive-gpms.categorical :as categorical]
+            [gensql.inference.gpm.primitive-gpms.gaussian :as gaussian]))
 
 (defn primitive?
   "Checks whether the given GPM is a primitive GPM."