Merge branch 'master' into 4.2

statnet · Oct 8, 2024 · fae00be · fae00be
2 parents d140653 + 691c72d
commit fae00be
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,4 @@ Rplots.pdf
 ^revdep$
 ^README.md$
 ^man-roxygen$
+^CODE_OF_CONDUCT\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -28,6 +28,9 @@
 #   debug: compile package with -DDEBUG and -UNDEBUG
 #
 #   covr: run in covr mode may be used with 'full' but probably not with others.
+#
+#
+# Typical public, private, and release configurations are provided in the variables below.
 
 on: [push, pull_request]
 
@@ -37,6 +40,21 @@ name: R-CMD-check
 env:
   PUBLIC: ''
   PRIVATE: ''
+  PUBLIC_CONFIG: '{"config":[
+            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug"},
+            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}'
+  RELEASE_CONFIG: '{"config":[
+            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, vignettes, remote, strict"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, vignettes, remote, strict"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"},
+            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr, strict"}]}'
+  PRIVATE_CONFIG: '{"config":[
+            {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"}
+            ]}'
 
 jobs:
   Set-Matrix-Private:
@@ -76,17 +94,10 @@ jobs:
         run: |
           if [[ "${{ env.IAM }}" == 'public' ]] # Public: full set.
           then
-            config='{"config":[
-            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, remote, vignettes, strict"},
-            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, remote, vignettes, strict"},
-            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"},
-            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"},
-            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}'
+            config='${{ env.RELEASE_CONFIG }}'
           elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set.
           then
-            config='{"config":[
-            {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"}
-            ]}'
+            config='${{ env.PRIVATE_CONFIG }}'
           else # Private with public analogue: no checking.
             config=''
           fi
@@ -123,7 +134,7 @@ jobs:
           fi
         shell: bash
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -148,6 +159,7 @@ jobs:
             any::rcmdcheck
             any::covr
             any::V8
+            any::xml2
           needs: |
             check
             coverage
@@ -169,7 +181,7 @@ jobs:
 
       - name: Upload build results
         if: contains(matrix.config.flags, 'binaries') && !failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-binaries
           path: binaries
@@ -243,7 +255,7 @@ jobs:
 
       - name: Upload check results
         if: contains(matrix.config.flags, 'covr') == false && failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: |
@@ -257,5 +269,22 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: ${{ runner.os != 'macOS' }} # Rmpi is not available on macOS.
           ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }}
-        run: covr::codecov(type=c("tests","examples"))
+        run: |
+          cov <- covr::package_coverage(
+            type=c("tests", "examples"),
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - name: Upload coverage results
+        if: contains(matrix.config.flags, 'covr')
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at contact@statnet.org. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tergm
-Version: 4.2.0
-Date: 2023-05-30
+Version: 4.2.1
+Date: 2024-10-08
 Title: Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
 Authors@R: c(
         person(c("Pavel", "N."), "Krivitsky", role=c("aut","cre"), email="pavel@statnet.org", comment=c(ORCID="0000-0002-9101-3362")),
@@ -14,38 +14,39 @@ Authors@R: c(
         person("Skye", "Bender-deMoll", role=c("ctb"), email="skyebend@skyeome.net"),
         person("Li","Wang",role=c("ctb"),email="lxwang@gmail.com"),
         person("Kirk","Li",role=c("ctb"),email="kirkli@uw.edu"),
-        person("Chad", "Klumb", role=c("ctb"), email="cklumb@gmail.com"))
+        person("Chad", "Klumb", role=c("ctb"), email="cklumb@gmail.com"),
+        person("Adrien", "Le Guillou", role=c("ctb"), email="git@aleguillou.org", comment=c(ORCID="0000-0002-4791-418X")))
 Depends:
-    ergm (>= 4.5.0),
-    network (>= 1.18.0),
-    networkDynamic (>= 0.11.3)
+    ergm (>= 4.7.0),
+    network (>= 1.18.2),
+    networkDynamic (>= 0.11.4)
 Imports:
+    robustbase (>= 0.95),
+    coda (>= 0.19-4.1),
+    statnet.common (>= 4.10.0),
+    ergm.multi (>= 0.2.1),
+    purrr (>= 1.0.2),
     methods,
     utils,
-    robustbase (>= 0.93.5),
-    coda (>= 0.19.2),
-    nlme (>= 3.1.139),
-    MASS (>= 7.3.51.4),
-    statnet.common (>= 4.9.0),
-    ergm.multi (>= 0.2.0),
-    purrr
+    nlme,
+    MASS
 LinkingTo:
     ergm
 Suggests:
-    lattice (>= 0.20.38),
-    parallel,
-    rmarkdown (>= 1.12),
-    knitr (>= 1.22),
-    tibble,
-    testthat,
-    covr,
-    networkLite
+    rmarkdown (>= 2.28),
+    knitr (>= 1.48),
+    tibble (>= 3.2.1),
+    testthat (>= 3.2.1.1),
+    covr (>= 3.6.4),
+    networkLite (>= 1.0.5),
+    lattice,
+    parallel
 BugReports: https://github.com/statnet/tergm/issues
 Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.
 License: GPL-3 + file LICENSE
 URL: https://statnet.org
 VignetteBuilder: rmarkdown, knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2.9000
 Roxygen: list(markdown = TRUE)
 Config/testthat/parallel: true
 Config/testthat/edition: 3

diff --git a/LICENSE b/LICENSE
@@ -37,4 +37,4 @@ Martina Morris, University of Washington
 
 The 'statnet' development team
 
-Copyright 2008-2023
+Copyright 2008-2024
diff --git a/R/InitErgmConstraint.hints.R b/R/InitErgmConstraint.hints.R
@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2023 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 
 #' @templateVar name discord

diff --git a/R/InitErgmProposal.DynMLE.R b/R/InitErgmProposal.DynMLE.R
@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2023 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 
 #' @templateVar name staticDiscordTNT

diff --git a/R/InitErgmProposal.DynMoME.R b/R/InitErgmProposal.DynMoME.R
@@ -5,14 +5,14 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2008-2023 Statnet Commons
+#  Copyright 2008-2024 Statnet Commons
 ################################################################################
 
 #' @templateVar name discordTNT
 #' @aliases InitErgmProposal.discordTNT
 #' @title Temperal TNT proposal
 #' @description A temporal version of \code{\link[ergm:TNT-ergmProposal]{TNT}}, with approximately
-#'   code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
+#'   \code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
 #'   approximately \code{1 - discordance_fraction} of proposed toggles being TNT proposals from
 #'   network.  The value of \code{discordance_fraction} can be set by the user as a proposal argument,
 #'   defaults to `0.5`.
@@ -32,7 +32,7 @@ InitErgmProposal.discordTNT <- function(arguments, nw, ...) {
 #' @templateVar name discordBDStratTNT
 #' @aliases InitErgmProposal.discordBDStratTNT
 #' @title Temperal TNT proposal with degree bounds
-#' @description A temporal version of \code{\link[ergm:ergm-proposals]{BDStratTNT}}.  Within each
+#' @description A temporal version of \code{\link[ergm:BDStratTNT-ergmProposal]{BDStratTNT}}.  Within each
 #'   mixing type, approximately 50\% of proposed toggles are made on
 #'   dyads, and approximately 50\% of proposed toggles are
 #'   proposals from the network, all subject to the bounded degree
@@ -42,7 +42,7 @@ InitErgmProposal.discordTNT <- function(arguments, nw, ...) {
 #'
 #'   arguments are the same as for \code{\link[ergm:BDStratTNT-ergmProposal]{BDStratTNT}},
 #'   and should be passed in via the \code{\link[ergm:bd-ergmConstraint]{bd}} and
-#'   code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
+#'   \code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
 #'   \code{\link[ergm:strat-ergmHint]{strat}} hint.
 #' @template ergmProposal-general
 NULL
Original file line number	Diff line number	Diff line change
Expand Up		@@ -37,4 +37,4 @@ Martina Morris, University of Washington

		The 'statnet' development team

		Copyright 2008-2023
		Copyright 2008-2024