Merge pull request #224 from se-sic/dev

Version 4.1

Merged-by: Thomas Bock <[email protected]>

.drone.yml

@@ -11,7 +11,7 @@
 ## with this program; if not, write to the Free Software Foundation, Inc.,
 ## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 ##
-## Copyright 2020-2021 by Thomas Bock <[email protected]>
+## Copyright 2020-2022 by Thomas Bock <[email protected]>
 ## All Rights Reserved.
 
 # Drone CI Setup
@@ -27,12 +27,17 @@ platform:
 
 steps:
 - name: R-latest
-  image: r-base:latest
+  image: rocker/r-ver:latest
   commands: &runTests
   # stop treating warnings as errors
   - unset CI
   # package dependencies
-  - apt install update -y && libudunits2-dev
+  #  - apt install update -y && libudunits2-dev
+  - apt-get update -y
+  - apt-get install --assume-yes libxml2
+  - apt-get install --assume-yes libxml2-dev
+  - apt-get install --assume-yes libglpk-dev
+  - echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >>"/usr/local/lib/R/etc/Rprofile.site"
   # package installation
   - Rscript install.R
   # execute test suite
@@ -41,37 +46,31 @@ steps:
 
 - name: R-4.1
   pull: if-not-exists
-  image: r-base:4.1.1
+  image: rocker/r-ver:4.1.3
   commands: *runTests
   depends_on: [clone]
 
 - name: R-4.0
   pull: if-not-exists
-  image: r-base:4.0.5
+  image: rocker/r-ver:4.0.5
   commands: *runTests
   depends_on: [clone]
 
 - name: R-3.6
   pull: if-not-exists
-  image: r-base:3.6.3
+  image: rocker/r-ver:3.6.3
   commands: *runTests
   depends_on: [clone]
 
 - name: R-3.5
   pull: if-not-exists
-  image: r-base:3.5.3
+  image: rocker/r-ver:3.5.3
   commands: *runTests
   depends_on: [clone]
 
 - name: R-3.4
   pull: if-not-exists
-  image: r-base:3.4.4
-  commands: *runTests
-  depends_on: [clone]
-
-- name: R-3.3
-  pull: if-not-exists
-  image: r-base:3.3.2
+  image: rocker/r-ver:3.4.4
   commands: *runTests
   depends_on: [clone]
 
@@ -87,12 +86,17 @@ platform:
 
 steps:
 - name: R-latest
-  image: r-base:latest
+  image: rocker/r-ver:latest
   commands: &runShowcase
   # stop treating warnings as errors
   - unset CI
   # package dependencies
-  - apt install update -y && libudunits2-dev
+  #- apt install update -y && libudunits2-dev
+  - apt-get update -y
+  - apt-get install --assume-yes libxml2
+  - apt-get install --assume-yes libxml2-dev
+  - apt-get install --assume-yes libglpk-dev
+  - echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >>"/usr/local/lib/R/etc/Rprofile.site"
   # package installation
   - Rscript install.R
   # execute showcase file
@@ -101,40 +105,33 @@ steps:
 
 - name: R-4.1
   pull: if-not-exists
-  image: r-base:4.1.0
+  image: rocker/r-ver:4.1.3
   commands: *runShowcase
   depends_on: [clone]
 
 - name: R-4.0
   pull: if-not-exists
-  image: r-base:4.0.5
+  image: rocker/r-ver:4.0.5
   commands: *runShowcase
   depends_on: [clone]
 
 - name: R-3.6
   pull: if-not-exists
-  image: r-base:3.6.3
-  commands: *runShowcase
-  depends_on: [clone]
-
-- name: R-3.5
-  pull: if-not-exists
-  image: r-base:3.5.3
-  commands: *runShowcase
-  depends_on: [clone]
-
-- name: R-3.4
-  pull: if-not-exists
-  image: r-base:3.4.4
-  commands: *runShowcase
-  depends_on: [clone]
-
-- name: R-3.3
-  pull: if-not-exists
-  image: r-base:3.3.2
+  image: rocker/r-ver:3.6.3
   commands: *runShowcase
   depends_on: [clone]
 
+#- name: R-3.5
+#  pull: if-not-exists
+#  image: rocker/r-ver:3.5.3
+#  commands: *runShowcase
+#  depends_on: [clone]
+#
+#- name: R-3.4
+#  pull: if-not-exists
+#  image: rocker/r-ver:3.4.4
+#  commands: *runShowcase
+#  depends_on: [clone]
 
 #trigger:
 #  branch:

NEWS.md

@@ -2,6 +2,21 @@
 
 # coronet – Changelog
 
+## 4.1
+
+### Added
+- Incorporate gender data, i.e., add a configuration entry to the project configuration, add function `read.gender` for reading gender data, add functions `get.gender` and `set.gender` and corresponding utility functions to automatically merge gender data to the author data (PR #216, 8868ff47900cf804553ec98683b736b07350fc64, bfbe4deb9d14faeed56bdf37f9f732e01c41af57, 0a23862c6308c27fe4f93835c3a4480eac03ca91, a7744b548ac5ab697a4eb3d71987ddedef180d59, 6a50fd15bdd6382fa3d868a21a41a4b0a36ffce7, 413e24c18532d06144ef996184192594a0893ca3, 39db3158e931fa627e974451ae66c57bd0b77b12, 1e4026def1995a23b3f42eac5eb343ee5a518798)
+
+### Changed/Improved
+- Add `mode` parameter to `metrics.vertex.degrees` to allow choosing between indegree, outdegree, and total (#219, ae14eb4cb83c6ab8f387886228cdf7ea6f3258c4)
+- Adjust `.drone.yml` CI config to prevent pipeline fails: `R` version `3.3` is not tested any more as some packages are not available any more for this `R` version (ca6b474d773c045dd88a19aee905283a373df0a6). Also another docker container in the CI pipeline is used as there are problems with the previously used docker instance (937f797ee04b78a087ea84043d075e7ca7558d70)
+
+### Fixed
+- Fix values in test for the eigenvector centrality as igraph has changed the calculation of this with version 1.2.7. Also put a warning that we recommend version 1.3.0 in `install.R` and document it in the `README.md` (25fb86277c7cc15b94ca0327bff4bb7e818ca09b, 1bcbca96d6dbaa2d4a28e830da963604682eac70)
+- Fix the filtering of the deleted user in `util-read.R` to always be lowercase as the deleted user can appear with different spellings (#214, 1b4072c7ec0e33a595e31d9e9d27bb5c133b1556)
+- Add check to `get.first.activity.data` to look for missing activity types. If no activities are in the RangeData, the function will print a warning and return an empty list (PR #220, #217, 5707517600c5579095c245b63c745d01cde02799, 42a4befb36e7fd9830924dc7fb2e04ecdf86e209,  d6424c03baff05562448df1b6b87828ca9a37b88, ca8a1b4c628261dcb471e1da3603439e75e4cc56, f6553c6106e5fec3837c6edb906a4d0960c5c5fb)
+
+
 ## 4.0
 
 ### Announcement
@@ -15,7 +30,7 @@
 - Add function `get.data.sources.from.relations` to `util-networks.R` which extracts the data sources of a network that were used when building it (PR #195, d1e4413a49ab83a115a7f26719592876371ab264)
 - Add tests for the `get.data.sources.from.relations` function (PR #195, add0c746dde8279da41d180deecf52b91a46095c)
 - Add logo directory containing several logo variants (PR #196, 82f99719b8a43b0a44914b67b26bf1a34bb076c6, dc4659ea354e97159f8ee6167811db544f0b7087, fdc5e677325225f92d1f99948cb9441bfe1d150d, 752a9b376ffeffd5d6b380b4fdba838a890e3ef7)
-- Add function `preprocess.issue.data`, which implements common issue data filtering operations. (fcf5cee64c809d62a33275cbd3272b8087869eea, a566caec6d7e649cc495d292a19eca8a7ffccde8, 5ba6feb988c44e2ba398bccce6c88e69d3bb552e)
+- Add function `preprocess.issue.data`, which implements common issue data filtering operations (fcf5cee64c809d62a33275cbd3272b8087869eea, a566caec6d7e649cc495d292a19eca8a7ffccde8, 5ba6feb988c44e2ba398bccce6c88e69d3bb552e)
 - Add function `get.issues.uncached`, which gets the issues filtered without poisoning or using the cache. (eb919fad9519d6e1a23261977bb3bfa2b899aaf9)
 - Add function `get.issues.unfiltered` to get the unfiltered issues so that these methods follow the naming scheme known from the respective methods for commits (b9dd94c8575b8cab40d0d1185368854f84299d87, e05f3448e1e2e8faaac219ed4ac818f82f3d8ff7)
 - Add per-author vertex attributes regarding counting of issues, issue-creations, issue-comments, mails, mail-threads, ... (like mail thread count, issue creation count) (PR #194, issue #188, 9f9150a97ffbb64607df0ddcbce299e16c2580da, 7260d62cf6f1470584753f76970d19664638eeed, 139f70b67903909bcd4c57e26afa458681a869f2, eb4f649c04155e22195627072e0f08bb8fe65dc4, 627873c641410182ca8fee0e78b95d7bda1e8e6b, 1e1406f4a0898cac3e61a7bc9a5aa665dceef79f, 98e11abc651b5fe0ec994eddea078635b0d6f0b2, a566caec6d7e649cc495d292a19eca8a7ffccde8)

README.md

@@ -59,9 +59,9 @@ While using the package, we require the following infrastructure.
 
 #### [`R`](https://www.r-project.org/)
 
-Minimum requirement is `R` version `3.3.1`. Hence, later `R` versions also work.
+Minimum requirement is `R` version `3.4.4`. Hence, later `R` versions also work. (Earlier `R` versions beginning from version `3.3.1` on should also work, but some packages are not available any more for these versions, so we do not test them any more in our CI pipeline.)
 
-We currently recommend version `4.1.1` or `3.6.3` for reliability reasons and `packrat` compatibility, but also later `R` versions should work (and are tested using our CI script).
+We currently *recommend* `R` version `4.1.1` or `3.6.3` for reliability reasons and `packrat` compatibility, but also later `R` versions should work (and are tested using our CI script).
 
 #### [`packrat`](http://rstudio.github.io/packrat/) (recommended)
 
@@ -125,7 +125,7 @@ Alternatively, you can run `Rscript install.R` to install the packages.
 
 - `yaml`: To read YAML configuration files (i.e., Codeface configuration files)
 - `R6`: For proper classes
-- `igraph`: For the construction of networks
+- `igraph`: For the construction of networks (package version `1.3.0` or higher is recommended)
 - `plyr`: For the `dlply` splitting-function and `rbind.fill`
 - `parallel`: For parallelization
 - `logging`: Logging
@@ -192,6 +192,7 @@ There are two distinguishable types of data sources that are both handled by the
         1. `none` is the default value and does not impact the configuration at all.
         2. `title` merges the commit message titles (i.e. the first non white space line of a commit message) to the commit data. This gives the data frame an additional column `title`.
         3. `messages` merges both titles and message bodies to the commit data frame. This adds two new columns `title` and `message`.
+    * Gender data of authors (see also the parameter `gender` in the [`ProjectConf`](#configurable-data-retrieval-related-parameters) class)))
     * [PaStA](https://github.com/lfd/PaStA/)  data (patch-stack analysis, see also the parameter `pasta` in the [`ProjectConf`](#configurable-data-retrieval-related-parameters) class))
         * Patch-stack analysis to link patches sent to mailing lists and upstream commits
     * Synchronicity information on commits (see also the parameter `synchronicity` in the [`ProjectConf`](#configurable-data-retrieval-related-parameters) class)
@@ -557,6 +558,9 @@ There is no way to update the entries, except for the revision-based parameters.
 - `filter.bots`
     * Remove all commits, issues, and mails made by bots. Bots are identified using the `bots.list` file.
     * [`TRUE`, *`FALSE`*]
+- `gender`
+    * Read and add gender data to authors (column `gender`)
+    * [`TRUE`, *`FALSE`*]
 - `issues.only.comments`
     * Only use comments from the issue data on disk and no further events such as references and label changes
     * [*`TRUE`*, `FALSE`]

install.R

@@ -16,8 +16,10 @@
 ## Copyright 2015 by Wolfgang Mauerer <[email protected]>
 ## Copyright 2015-2017 by Claus Hunsen <[email protected]>
 ## Copyright 2017 by Thomas Bock <[email protected]>
+## Copyright 2022 by Thomas Bock <[email protected]>
 ## Copyright 2020-2021 by Thomas Bock <[email protected]>
 ## Copyright 2019 by Anselm Fehnker <[email protected]>
+## Copyright 2021 by Christian Hechtl <[email protected]>
 ## All Rights Reserved.
 ##
 ## Adapted from https://github.com/siemens/codeface/blob/be382e9171fb91b4aa99b99b09b2ef64a6dba0d5/packages.r
@@ -62,4 +64,9 @@ if (length(p) > 0) {
 
     ## set dependencies to 'NA' to install only necessary dependencies (i.e., "Depends", "Imports", "LinkingTo")
     install.packages(p, dependencies = NA, verbose = TRUE, quiet = TRUE)
+
+    igraph.version = installed.packages()[rownames(installed.packages()) == "igraph", "Version"]
+    if (compareVersion(igraph.version, "1.3.0") == -1) {
+        print("WARNING: igraph version 1.3.0 or higher is recommended for using coronet.")
+    }
 }

sample/results/testing/sample_gender/gender

@@ -0,0 +1,6 @@
+D1;male
+D2;female
+D3;male
+D4;male
+D5;female
+D6;female

tests/README.md

@@ -12,6 +12,7 @@ We have two test projects you can use when writing your tests:
      * Issues
      * Authors
      * Bots
+     * Gender
      * Commit messages
      * Pasta
      * Synchronicity

tests/codeface-data/results/testing/test_gender/gender.list

@@ -0,0 +1,9 @@
+Thomas;male
+Olaf;female
+Karl;male
+Max;male
+udo;female
+Björn;male
+georg;male
+Hans;male
+Fritz [email protected];unknown