Merge pull request #73 from dotemacs/tidy-up

Tidy up namespaces, doc strings, and whitespaces.

Author: adamtornhill

README.md

@@ -68,11 +68,11 @@ To analyze our VCS data we need to define a temporal period of interest. Over ti
 
 The first options is the legacy format used in Your Code As A Crime Scene. Use the `-c git` parse option when [Running Code Maat](#running-code-maat).
 
-          git log --pretty=format:'[%h] %aN %ad %s' --date=short --numstat --after=YYYY-MM-DD
+          git log --pretty=format:'[%h] %aN %ad %s' --date=short --numstat --after=YYYY-MM-DD > logfile.log
 
 There's a second supported Git format as well. It's more tolerant and faster to parse, so please prefer it over the plain `git` format described above. Use the `-c git2` parse option when [Running Code Maat](#running-code-maat).
 
-          git log --all --numstat --date=short --pretty=format:'--%h--%ad--%aN' --no-renames --after=YYYY-MM-DD
+          git log --all --numstat --date=short --pretty=format:'--%h--%ad--%aN' --no-renames --after=YYYY-MM-DD > logfile.log
 
 Many codebases include third-party content or non-code artefacts,  which might generate noise in the analyses.
 You can exclude such content via git's pathspecs that limit paths on the command line.
@@ -91,7 +91,7 @@ To exclude multiple folders, you just append more pathspecs:
 #### Generate a Perforce log file using the following command:
 
           p4 changes -s submitted -m 5000 //depot/project/... | cut -d ' ' -f 2 | xargs -I commitid -n1 sh -c 'p4 describe -s commitid | grep -v "^\s*$" && echo ""'
-          
+
 #### Generate a TFS log file using the following command from a Developer command-prompt:
 ###### Note:  The TFS CLI tool does not support custom date formatting.  The parser currently only supports the en-us default:  Friday, January 1, 2016 1:12:35 PM - you may need to adjust your system locale settings before using the following command.
 
@@ -118,9 +118,9 @@ When invoked with `-h`, Code Maat prints its usage:
              adam$ java -jar code-maat-0.9.0.jar
              This is Code Maat, a program used to collect statistics from a VCS.
              Version: 0.9.0-SNAPSHOT
-             
+
              Usage: program-name -l log-file [options]
-             
+
              Options:
                -l, --log LOG                                         Log file with input data
                -c, --version-control VCS                             Input vcs module type: supports svn, git, git2, hg, p4, or tfs

src/code_maat/analysis/authors.clj

@@ -67,7 +67,7 @@
         (ds/-order-by [:n-authors :n-revs] order-fn))))
 
 (defn all-authors
-  [ds options]
+  [ds]
   (->> ds
        all
        (ds/-dataset [:author])

src/code_maat/analysis/code_age.clj

@@ -6,9 +6,7 @@
 (ns code-maat.analysis.code-age
   (:require [code-maat.dataset.dataset :as ds]
             [code-maat.parsers.time-parser :as tp]
-            [clj-time.core :as tc]
-            [clojure.string :as str]
-            [code-maat.analysis.math :as math]))
+            [clj-time.core :as tc]))
 
 ;;; The following analysis is inspired by Dan North's presentation
 ;;; on keeping a short software half-life.
@@ -72,4 +70,3 @@
    (entities-by-latest-modification (time-now options))
    (ds/-dataset [:entity :age-months])
    (ds/-order-by [:age-months] :asc)))
-  

src/code_maat/analysis/commit_messages.clj

@@ -5,15 +5,14 @@
 
 (ns code-maat.analysis.commit-messages
   (:require [code-maat.dataset.dataset :as dataset]
-            [incanter.core :as incanter]
-            [code-maat.analysis.math :as math]))
+            [incanter.core :as incanter]))
 
 ;;; This module helps you analyze version-control data
 ;;; based on commit messages.
 ;;; Our commit messages contain information about our process and
 ;;; the kind of work we do.
 ;;; For example, we can use that information to extract
-;;; statistics on bug distributions. Note that this data is 
+;;; statistics on bug distributions. Note that this data is
 ;;; heuristics, not absolute truths (for that you need to mine
 ;;; your bug tracking system).
 ;;;

src/code_maat/analysis/communication.clj

@@ -8,8 +8,7 @@
             [code-maat.analysis.effort :as effort]
             [clojure.math.combinatorics :as combo]
             [code-maat.analysis.math :as m]
-            [clojure.math.numeric-tower :as math]
-            [incanter.core :as incanter]))
+            [clojure.math.numeric-tower :as math]))
 
 ;;; This module attempts to give some heuristics on
 ;;; the communication needs of a project.
@@ -34,7 +33,7 @@
 ;;; give us a fast way to look-up the total number of
 ;;; commits for an author.
 
-(defn- authorship-combos 
+(defn- authorship-combos
   [authors]
   (combo/selections authors 2))
 
@@ -89,7 +88,7 @@
    shared work by the authors on different entities.
    Returns a dataset containing pairs of all permutations
    of authors with a (heuristic) communication strength
-   value for each pair." 
+   value for each pair."
   [ds options]
   (->>
    (effort/as-revisions-per-author ds options)
@@ -99,4 +98,3 @@
    with-commit-stats
    (ds/-dataset [:author :peer :shared :average :strength])
    (ds/-order-by [:strength :author] :desc)))
-

src/code_maat/analysis/coupling_algos.clj

@@ -6,9 +6,8 @@
 (ns code-maat.analysis.coupling-algos
   (:require [clojure.math.combinatorics :as combo]
             [code-maat.dataset.dataset :as ds]
-            [code-maat.analysis.math :as m]
-            [clojure.math.numeric-tower :as math])
-  (:use incanter.core))
+            [clojure.math.numeric-tower :as math]
+            [incanter.core :as incanter]))
 
 ;;; This module contains the shared algorithms for the
 ;;; different coupling measures.
@@ -35,13 +34,13 @@
   (->
    (combo/selections entities 2)
    drop-mirrored-modules))
-   
+
 (defn as-entities-by-revision
   "Extracts the change set per revision
    from an Incanter dataset."
   [ds]
   (->>
-   ($ [:rev :entity] ds) ; minimal
+   (incanter/$ [:rev :entity] ds) ; minimal
    (ds/-group-by :rev)
    (map second)))
 
@@ -69,7 +68,7 @@
    its number of revisions as value.
    This is used when calculating the degree
    of coupling later."
-  [all-co-changing] 
+  [all-co-changing]
   (->
    (mapcat modules-in-one-rev all-co-changing)
    frequencies))
@@ -89,10 +88,10 @@
    (map as-co-changing-modules)))
 
 (defn coupling-frequencies
-  [co-changing]
   "Returns a map with pairs of coupled
    modules (pairs) as keyes and their
    number of shared revisions as value."
+  [co-changing]
   (->
    (apply concat co-changing)
    drop-duplicates ; remember: included to get the right total revisions

src/code_maat/analysis/effort.clj

@@ -5,7 +5,6 @@
 
 (ns code-maat.analysis.effort
   (:require [code-maat.dataset.dataset :as ds]
-            [incanter.core :as incanter]
             [clojure.math.numeric-tower :as m]
             [code-maat.analysis.math :as math]))
 

src/code_maat/analysis/logical_coupling.clj

@@ -7,8 +7,8 @@
   (:require [code-maat.analysis.coupling-algos :as c]
             [code-maat.dataset.dataset :as ds]
             [code-maat.analysis.math :as m]
-            [clojure.math.numeric-tower :as math])
-  (:use incanter.core))
+            [clojure.math.numeric-tower :as math]
+            [incanter.core :as incanter]))
 
 ;;; This module calculates the logical coupling of all modules.
 ;;;
@@ -48,11 +48,10 @@
    the number of shared commits between coupled entities divided
    by the average number of total commits for the coupled entities."
   ([ds options]
-     (by-degree ds options :desc))
+   (by-degree ds options :desc))
   ([ds options order-fn]
-     (->>
-      (partial c/within-threshold? options)
-      (as-logical-coupling-measure ds options)
-      (ds/-dataset [:entity :coupled :degree :average-revs])
-      ($order [:degree :average-revs] order-fn))))
-
+   (->>
+    (partial c/within-threshold? options)
+    (as-logical-coupling-measure ds options)
+    (ds/-dataset [:entity :coupled :degree :average-revs])
+    (incanter/$order [:degree :average-revs] order-fn))))

src/code_maat/analysis/math.clj

@@ -3,8 +3,7 @@
 ;;; Distributed under the GNU General Public License v3.0,
 ;;; see http://www.gnu.org/licenses/gpl.html
 
-(ns code-maat.analysis.math
-  (:require [clojure.math.numeric-tower :as m]))
+(ns code-maat.analysis.math)
 
 (defn average [& vals]
   (/

src/code_maat/analysis/sum_of_coupling.clj

@@ -5,8 +5,8 @@
 
 (ns code-maat.analysis.sum-of-coupling
   (:require [code-maat.dataset.dataset :as ds]
-            [code-maat.analysis.coupling-algos :as c])
-  (:use incanter.core))
+            [code-maat.analysis.coupling-algos :as c]
+            [incanter.core :as incanter]))
 
 ;;; This module calculates the sum of the temporal coupling for each module.
 ;;;
@@ -38,8 +38,8 @@
    (mapcat counted-entities)))
 
 (defn as-soc
-  "Calculates a Sum of Coupling for each entity in 
-   the dataset that passes the threshold for minimum 
+  "Calculates a Sum of Coupling for each entity in
+   the dataset that passes the threshold for minimum
    number of revisions."
   [ds {:keys [min-revs]}]
   (->> ds
@@ -48,17 +48,17 @@
                  (update-in acc [e] (fnil + 0) n))
                {})
        (into [])
-       (filter (fn [[e n]] 
+       (filter (fn [[e n]]
                  (> n min-revs)))))
 
 (defn by-degree
   "Calculates the sum of coupling. Returns a seq
    sorted in descending order (default) or an optional,
    custom sorting criterion."
   ([ds options]
-     (by-degree ds options :desc))
+   (by-degree ds options :desc))
   ([ds options order-fn]
-     (->>
-      (as-soc ds options)
-      (ds/-dataset [:entity :soc])
-      ($order [:soc :entity] order-fn))))
+   (->>
+    (as-soc ds options)
+    (ds/-dataset [:entity :soc])
+    (incanter/$order [:soc :entity] order-fn))))