Preparation Release 2.5.1 (#156)

* repaired test when pcbo is present: clojure is not mutable (#148) * repaired test when pcbo is present: clojure is not mutable * Classic 'Vorzeichenfehler' * New fca style (#149) * new latex fca style output format * removed whitespaces * Added doc string * Adapted requirements: now boring code but no warning * Ordinal motifs (#151) * Ordinal Motifs * reduce computational time for candidates-by-subset-heredity and identify-full-scale-measures :interordinal * add tests for ordinal-motifs * add is-of-scale? method to check if context is of specific scale-type * add documentation for ordinal motifs * test cycles-of-g * test scale-complex function * more tests for ordinal-motifs * add tests for get-complex * fix error in restrict-extents-to-base-set * Revert "fix error in restrict-extents-to-base-set" This reverts commit e11f5d0. * fix error in ordinal scale measures * stop compute-ordinal-motifs+stats at empty set to avoid error * add test for greedy-motif-covering * comment * Updated Authors * more boring imports --------- Co-authored-by: Johannes Hirth <[email protected]> Co-authored-by: Jana <[email protected]> * Adapted version number * Update README.md Updated year * Simplicial complexes (#153) * Ordinal Motifs * reduce computational time for candidates-by-subset-heredity and identify-full-scale-measures :interordinal * add tests for ordinal-motifs * add is-of-scale? method to check if context is of specific scale-type * add documentation for ordinal motifs * test cycles-of-g * test scale-complex function * more tests for ordinal-motifs * add tests for get-complex * fix error in restrict-extents-to-base-set * Revert "fix error in restrict-extents-to-base-set" This reverts commit e11f5d0. * fix error in ordinal scale measures * stop compute-ordinal-motifs+stats at empty set to avoid error * start adding structure for simplicial complexes * add test for greedy-motif-covering * comment * add and test FullSimplicialComplex * add constructor without check and more tests * add constructors * add function to create t-simplex from context and lattice * add another test example and fix some errors * experiments with next_closure for t-simplex * test t-simplex computation with next closure algorithm * generalize next-closure function (add ordinal motif case with :ordinal scale) * refactoring * more code cleanup * fix error in next closure for ordinal motifs * refactoring: move closed set functions from base to separate file * replace fca/next-closure with already existing methods * for :ordinal ordinal motifs with next closure, use same condition as in ordinal-motifs branch * add :interordinal, :nominal and :contranominal ordinal motifs with next closure * add more complex tests for ordinal motifs with next closure * simplify tests * refactoring and code cleanup * add :crown ordinal motifs with next closure * fix failing tests * remove :crown from simplicial complexes (because it is not a simplicial complex) * Fixed imports --------- Co-authored-by: Johannes Hirth <[email protected]> Co-authored-by: Jana <[email protected]> * Update Getting-Started.org * Update Getting-Started.org * Added complex-dimension * Added some analytics for simplicial complexes * Update deps-lock.json (#155) Co-authored-by: tomhanika <[email protected]> --------- Co-authored-by: Johannes Hirth <[email protected]> Co-authored-by: Johannes Hirth <[email protected]> Co-authored-by: Jana <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: tomhanika <[email protected]>
tomhanika · Aug 13, 2024 · 46b131a · 46b131a
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diff --git a/AUTHORS.md b/AUTHORS.md
@@ -11,7 +11,7 @@ Additional Contributors are
 * Immanuel Albrecht     (Context Editor Plugin for the GUI)
 * Sebastian Benner      (API)
 * Stefan Borgwardt      (Shared Intents)
-* Jana Fischer          (json format,Ordinal Motifs, scale-measures)
+* Jana Fischer          (json format, Simplicial Complex, Ordinal Motifs, scale-measures)
 * Tom Hanika            (Concept Probability)
 * Johannes Hirth        (pq-cores, Ordinal Motifs, scale-measures)
 * Gleb Kanterov         (interval-scale)

diff --git a/README.md b/README.md
@@ -94,7 +94,7 @@ would appreciate if you use the following reference.
 
 ## License
 
-Copyright ⓒ 2009—2018 Daniel Borchmann, 2018–2023 Tom Hanika
+Copyright ⓒ 2009—2018 Daniel Borchmann, 2018–2024 Tom Hanika
 
 Distributed under the Eclipse Public License.
 

diff --git a/deps-lock.json b/deps-lock.json
@@ -562,6 +562,26 @@
       "mvn-repo": "https://repo1.maven.org/maven2/",
       "hash": "sha256-KBRAgRJo5l2eJms8yJgpfiFOBPCXQNA4bO60qJI9Y78="
     },
+    {
+      "mvn-path": "net/mikera/clojure-pom/0.6.0/clojure-pom-0.6.0.pom",
+      "mvn-repo": "https://repo.clojars.org/",
+      "hash": "sha256-ApT9U7aW/29SAU5XUeJXiHii5kkP/SiwPHvX5A9/HVw="
+    },
+    {
+      "mvn-path": "net/mikera/core.matrix/0.63.0/core.matrix-0.63.0.jar",
+      "mvn-repo": "https://repo.clojars.org/",
+      "hash": "sha256-UCxlj7Q0EDgwxgDNCMAfPJdQPuwS2W6tklB4UwQAnuI="
+    },
+    {
+      "mvn-path": "net/mikera/core.matrix/0.63.0/core.matrix-0.63.0.pom",
+      "mvn-repo": "https://repo.clojars.org/",
+      "hash": "sha256-T3MYieJGpsINFq3W3PElUPj8pLEeW9Vjefa28UHeMcA="
+    },
+    {
+      "mvn-path": "net/mikera/mikera-pom/0.6.0/mikera-pom-0.6.0.pom",
+      "mvn-repo": "https://repo1.maven.org/maven2/",
+      "hash": "sha256-AzYO7a8+mxOHcZrgCf2V7mFF1nEO1P5QQ47IJxM5XTI="
+    },
     {
       "mvn-path": "nrepl/drawbridge/0.2.1/drawbridge-0.2.1.jar",
       "mvn-repo": "https://repo.clojars.org/",
@@ -992,6 +1012,11 @@
       "mvn-repo": "https://repo1.maven.org/maven2/",
       "hash": "sha256-IA0uyoZlJAy8uu5IwAcyS3tE02YIDpWN8dIujd4kg4w="
     },
+    {
+      "mvn-path": "org/clojure/clojure/1.10.1/clojure-1.10.1.pom",
+      "mvn-repo": "https://repo1.maven.org/maven2/",
+      "hash": "sha256-EPevJPoORzOE7RqAPgCpB0KzwA+Q3jW2uxXosW3YOow="
+    },
     {
       "mvn-path": "org/clojure/clojure/1.10.3/clojure-1.10.3.jar",
       "mvn-repo": "https://repo1.maven.org/maven2/",
@@ -1357,6 +1382,16 @@
       "mvn-repo": "https://repo1.maven.org/maven2/",
       "hash": "sha256-v7Yh5LAaW4vOEWpgcIQNzdWUnomceEaNgRtuiqqf0cc="
     },
+    {
+      "mvn-path": "org/clojure/tools.macro/0.1.5/tools.macro-0.1.5.jar",
+      "mvn-repo": "https://repo1.maven.org/maven2/",
+      "hash": "sha256-JxTXKUyQ+SaO7vNyj+TZjr+q7fJAoCN02u8rhVhEgkg="
+    },
+    {
+      "mvn-path": "org/clojure/tools.macro/0.1.5/tools.macro-0.1.5.pom",
+      "mvn-repo": "https://repo1.maven.org/maven2/",
+      "hash": "sha256-cGCU9H2ljugXofq5uAwxLs0nZHK85uHVRCOfFAcR2zE="
+    },
     {
       "mvn-path": "org/clojure/tools.namespace/0.2.11/tools.namespace-0.2.11.jar",
       "mvn-repo": "https://repo1.maven.org/maven2/",

diff --git a/doc/Getting-Started.org b/doc/Getting-Started.org
@@ -5,13 +5,13 @@
 
 ** Running conexp-clj from pre-compiled binaries
 
-To run ~conexp-clj~, a Java Runtime Environment with version ≥ 1.8 is necessary.
+To run ~conexp-clj~, a Java Runtime Environment with version ≥ 1.11 is necessary.
 The recommended way to use ~conexp-clj~ outside of development is to download a
-[[https://algebra20.de/conexp/][pre-compiled version]].  These are just usual Java jar files and can be used like
+[[https://github.com/tomhanika/conexp-clj/releases#:~:text=Assets][pre-compiled version]].  These are just usual Java jar files and can be used like
 this:
 
 #+begin_src sh :eval never
-java -jar conexp-clj-2.1.1-SNAPSHOT-standalone.jar
+java -jar conexp-clj-2.5.0-standalone-openjdk-11.jar
 #+end_src
 
 This will get you a prompt for ~conexp-clj~ much like
@@ -32,6 +32,13 @@ conexp.analysis=> (+ 1 1)
 (where you do not type the ~conexp.main=>~ and the 2 is the result of the
 evaluation.
 
+You may also start the (rudimentary) graphical user interface (GUI) by appending `-g` 
+
+#+begin_src sh :eval never 
+java -jar conexp-clj-2.5.0-standalone-openjdk-11.jar -g
+#+end_src
+
+
 ** Running conexp-clj directly from source
 
 It is also possible to get command line access for ~conexp-clj~ directly from
@@ -59,6 +66,12 @@ This will give you a command prompt as in the previous case.
 
 If you want a more sophisticated repl, you may try [[https://github.com/clojure-emacs/cider][Emacs Cider]].
 
+You can start the graphical user interface (GUI) via 
+
+#+begin_src sh :eval never
+lein run -g
+#+end_src
+
 ** Running conexp-clj via nix
 
 Using the [[https://nixos.org/manual/nix/stable/][nix]] package manager, you can directly run ~conexp-clj~ without
@@ -125,15 +138,9 @@ type into the prompt can also be written into a file, say ~file.clj~.  To run
 (load-file "file.clj")
 #+end_src
 
-** Graphical User Interface
-
-It is also possible to use ~conexp-clj~'s incomplete GUI fragment.  You can start it running the following code in you favourite shell
-
-#+begin_src sh :eval never
-java -jar conexp-clj-2.1.1-SNAPSHOT-standalone.jar -g
-#+end_src
+** Concerning the Graphical User Interface
 
-But please note that the GUI is not only (inherently) limited in its
+As indicated above, tt is also possible to use ~conexp-clj~'s incomplete GUI fragment. But please note that the GUI is not only (inherently) limited in its
 functionality, but also quite (not to say: really) buggy.
 
 ** Online Documentation (No Network Required!)

diff --git a/project.clj b/project.clj
@@ -7,7 +7,7 @@
 ;; You must not remove this notice, or any other, from this software.
 
 
-(defproject conexp-clj "2.5.0"
+(defproject conexp-clj "2.5.1-SNAPSHOT"
 
   :min-lein-version "2.0.0"
   :description "A ConExp rewrite in clojure -- and so much more ..."
@@ -17,6 +17,7 @@
             :url "http://www.eclipse.org/legal/epl-v10.html"}
   :dependencies [[org.clojure/clojure             "1.11.3"]
                  [org.clojure/core.async          "1.6.681"]
+                 [org.clojure/data.csv            "1.1.0"]
                  [org.clojure/data.int-map        "1.3.0"]
                  [org.clojure/data.json           "2.5.0"]
                  [org.clojure/data.xml            "0.0.8"]
@@ -42,7 +43,7 @@
                  [http-kit "2.8.0"]
                  [org.apache.commons/commons-math3 "3.6.1"]
                  [luposlip/json-schema             "0.4.5"]
-                 [org.clojure/data.csv "1.1.0"]]
+                 [net.mikera/core.matrix "0.63.0"]]
   :profiles {:uberjar {:main conexp.main
                        :dependencies [[javax.servlet/servlet-api "2.5"]
                                       [ring/ring-mock "0.4.0"]

diff --git a/src/main/clojure/conexp/analysis.clj b/src/main/clojure/conexp/analysis.clj
@@ -23,6 +23,7 @@
     [pqcores :refer :all]
     [protoconcepts :refer :all]
     [random-contexts :refer :all]
+    [simplicial-complexes :refer :all]
     [triadic-exploration :refer :all]]
    [conexp.math
     [algebra :refer :all]