v0.1.1

.Rbuildignore

@@ -18,3 +18,8 @@ vignettes/precompile\.R
 ^CRAN-SUBMISSION$
 ^README\.Rmd$
 ^.mailmap$
+^\.positai$
+^\.claude$
+^CLAUDE\.md$
+^\.Rhistory$
+^\.RData$

.github/pull_request_template.md

@@ -2,18 +2,7 @@
 
 # Checklist:
 
-- PR form
-  - [ ] Description above itemizes changes under subtitles, e.g. "## Data""
-  - [ ] Any closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"
-  - [ ] Package builds on my OS without issues
-- PR checks all pass for latest commit
-  - [ ] CodeFactor check: Package improves or maintains good style
-  - [ ] Package builds on Mac
-  - [ ] Package builds on Windows
-  - [ ] Package builds on Linux
-  - [ ] CodeCov check: Package improves or maintains good test coverage
 - Documentation
-  - [ ] Any new or modified functions or data have roxygen style documentation in their .R scripts
-  - [ ] Longer functions are commented inline or broken down into helper functions so that it is easier to debug in the future
+  - [ ] Longer functions are commented inline or broken down into helper functions to help debugging
+- PR form
   - [ ] PR description above and the NEWS.md file are aligned
-  - [ ] DESCRIPTION file version is bumped by the appropriate increment (major, minor, patch)

.github/workflows/prchecks.yml

@@ -24,11 +24,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -40,6 +42,7 @@ jobs:
             any::rcmdcheck
 
       - uses: r-lib/actions/check-r-package@v2
+        env:
           _R_CHECK_FORCE_SUGGESTS_: false
         with:
           upload-snapshots: true
@@ -53,13 +56,16 @@ jobs:
         shell: Rscript {0}
 
       - name: Save binary artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: ${{ matrix.config.asset_name }}
           path: build/
 
       - name: Calculate code coverage
-        run: Rscript -e "covr::codecov()"
+        if: runner.os == 'macOS'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        run: Rscript -e 'covr::codecov(token = Sys.getenv("CODECOV_TOKEN"))'
 
       - name: Lint
         run: lintr::lint_package()
@@ -68,3 +74,49 @@ jobs:
       - name: Spell check
         run: spelling::spell_check_package()
         shell: Rscript {0}
+
+  pr-metadata:
+    name: PR metadata checks
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+
+      - name: Check DESCRIPTION version is bumped
+        env:
+          BASE_SHA: ${{ github.event.pull_request.base.sha }}
+        run: |
+          BASE_VERSION=$(git show "$BASE_SHA:DESCRIPTION" | grep -m1 '^Version:' | sed 's/Version: *//')
+          HEAD_VERSION=$(grep -m1 '^Version:' DESCRIPTION | sed 's/Version: *//')
+          echo "Base version: $BASE_VERSION"
+          echo "Head version: $HEAD_VERSION"
+          if [ "$BASE_VERSION" = "$HEAD_VERSION" ]; then
+            echo "::error::DESCRIPTION Version has not been bumped from $BASE_VERSION"
+            exit 1
+          fi
+          HIGHEST=$(printf '%s\n%s\n' "$BASE_VERSION" "$HEAD_VERSION" | sort -V | tail -n1)
+          if [ "$HIGHEST" != "$HEAD_VERSION" ]; then
+            echo "::error::DESCRIPTION Version $HEAD_VERSION is not greater than base version $BASE_VERSION"
+            exit 1
+          fi
+
+      - name: Check PR title mentions the new version number
+        env:
+          PR_TITLE: ${{ github.event.pull_request.title }}
+        run: |
+          HEAD_VERSION=$(grep -m1 '^Version:' DESCRIPTION | sed 's/Version: *//')
+          if [[ "$PR_TITLE" != *"$HEAD_VERSION"* ]]; then
+            echo "::error::PR title does not mention the new version number ($HEAD_VERSION): \"$PR_TITLE\""
+            exit 1
+          fi
+
+      - name: Check PR description itemizes changes under subsection titles
+        env:
+          PR_BODY: ${{ github.event.pull_request.body }}
+        run: |
+          if ! grep -qE '^##[[:space:]]' <<< "$PR_BODY"; then
+            echo "::error::PR description does not itemize changes under subsection titles (e.g. \"## Data\")"
+            exit 1
+          fi

.github/workflows/pushrelease.yml

@@ -24,7 +24,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -55,14 +55,16 @@ jobs:
         shell: Rscript {0}
 
       - name: Save binary artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: ${{ matrix.config.asset_name }}
           path: build/
 
       - name: Calculate code coverage
-        if: runner.os == 'macOS-latest'
-        run: Rscript -e "covr::codecov()"
+        if: runner.os == 'macOS'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        run: Rscript -e 'covr::codecov(token = Sys.getenv("CODECOV_TOKEN"))'
 
   release:
     name: Bump version and release
@@ -73,7 +75,7 @@ jobs:
       contents: write
     steps:
       - name: Checkout one
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           fetch-depth: '0'
       - name: Bump version and push tag
@@ -85,15 +87,15 @@ jobs:
           DEFAULT_BUMP: patch
           RELEASE_BRANCHES: main
       - name: Checkout two
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Extract version
         run: |
           echo "PACKAGE_VERSION=$(grep '^Version' DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV
           echo "PACKAGE_NAME=$(grep '^Package' DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV
 
       - name: Download binaries
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
 
       - name: Rename binaries release
         shell: bash
@@ -104,13 +106,27 @@ jobs:
           cp ./winOS/${{ env.PACKAGE_NAME }}_${{ env.PACKAGE_VERSION }}*.zip .
           echo "Renamed files"
           ls infernet_*
-
+
+      - name: Extract release notes from NEWS.md
+        shell: bash
+        run: |
+          # Take the NEWS.md section for this version, else the topmost section.
+          awk -v ver="${{ env.PACKAGE_NAME }} ${{ env.PACKAGE_VERSION }}" '
+            /^# / { if (found) exit; if (substr($0, 3) == ver) { found = 1; next } }
+            found { print }
+          ' NEWS.md > RELEASE_NOTES.md
+          if [ ! -s RELEASE_NOTES.md ]; then
+            awk 'NR > 1 && /^# / { exit } NR > 1 { print }' NEWS.md > RELEASE_NOTES.md
+          fi
+          cat RELEASE_NOTES.md
+
       - name: Create Release and Upload Assets
         id: create_release
         uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ steps.newtag.outputs.tag }}
           name: Release ${{ steps.newtag.outputs.tag }}
+          body_path: RELEASE_NOTES.md
           draft: false
           prerelease: false
           fail_on_unmatched_files: true
@@ -120,7 +136,7 @@ jobs:
             infernet_*.tar.gz
             infernet_*.zip
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   pkgdown:
     name: Build and deploy website
@@ -130,11 +146,11 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -143,7 +159,7 @@ jobs:
             any::rcmdcheck
             any::pkgdown
             any::rsconnect
-          needs: check
+          needs: website
 
       - name: Install package
         run: R CMD INSTALL .

.gitignore

@@ -15,3 +15,4 @@ CRAN-SUBMISSION
 toadd/*
 .data.csv
 cache/*
+.positai

CLAUDE.md

@@ -0,0 +1,29 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project overview
+
+`infernet` is an R package (part of the [stocnet](https://github.com/stocnet) ecosystem) providing the *inferential layer* for network analysis: 
+conditional uniform graph (CUG) and quadratic assignment procedure (QAP) tests of network statistics, and multiple regression QAP (MRQAP).
+It combines a formula front end with a range of estimator range, missing-data handling, and treatments for multimodal, multilevel, and cognitive social structure networks.
+It builds on `{manynet}` (network classes and coercion) and `{netrics}` (measures), 
+so its functions accept matrices, edgelists, `{igraph}`, `{network}`, `{tidygraph}`, or `stocnet` objects, 
+and one-mode or two-mode networks alike.
+Plotting results belongs in `{autograph}`.
+
+Full package documentation — common dev commands, file organization, the `net_regression()` pipeline, 
+function body and parallelism conventions, console messaging, dependency practice, test conventions, `NEWS.md` conventions, and branching/CI — lives in [.github/CONTRIBUTING.md](.github/CONTRIBUTING.md).
+Read it before adding or restructuring functions, 
+or when you need the exact `devtools`/testing commands for this repo.
+
+Note that `{migraph}` still carries older copies of `net_regression()` and the `test_*()` family, 
+which `{infernet}` supersedes. 
+A fix made in `{migraph}` needs porting here; a fix made here does not need porting back.
+
+## Where to make changes
+
+- Make all changes on the `develop` branch. `develop` is the working branch; `main` is the release branch.
+- Do not commit to `main` directly. Do not open a new feature branch for a fix unless the user asks.
+- Keep changes reviewable. Leave them as an uncommitted working-tree diff on `develop`, or as local commits on `develop`. Commit only when the user asks.
+- Do not push to `origin/develop` without explicit approval. `develop` is shared.

DESCRIPTION

@@ -1,17 +1,25 @@
 Package: infernet
-Title: Basic inferential models for many different types of networks
-Version: 0.1.0
-Date: 2025-06-23
-Description: TBD.
+Title: Inferential Models for Many Different Types of Networks
+Version: 0.1.1
+Description: A set of tools for testing networks.
+   It includes functions for univariate and multivariate 
+   conditional uniform graph and quadratic assignment procedure testing,
+   and multiple regression quadratic assignment procedure (MRQAP) models
+   for a range of families, with random and fixed effects,
+   missing data, and cognitive social structures.
+   Built on the 'manynet' package, all functions operate with matrices, 
+   edge lists, and 'igraph', 'network', and 'tidygraph' objects,
+   and on one-mode and two-mode (bipartite) networks.
 URL: https://stocnet.github.io/infernet/
 BugReports: https://github.com/stocnet/infernet/issues
 License: MIT + file LICENSE
 Language: en-GB
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.3
 Depends: 
-    R (>= 3.6.0)
+    R (>= 4.1.0),
+    manynet (>= 2.3.1),
+    netrics (>= 1.0.1)
 Authors@R: 
     c(person(given = "James",
              family = "Hollway",
@@ -24,16 +32,11 @@ Authors@R:
              comment = c(ORCID = "0000-0003-4288-4732"))
     )
 Imports:
-    cli,
-    dplyr,
     furrr,
     future,
     future.apply,
-    manynet,
     purrr,
-    reformulas,
-    stats,
-    utils
+    reformulas
 Suggests:
     lme4,
     nnet,
@@ -56,3 +59,5 @@ Config/Needs/website:
     pkgdown
 Config/testthat/parallel: true
 Config/testthat/edition: 3
+Config/testthat/start-first: qap_estimators, model_tests
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -6,11 +6,12 @@ export(net_regression)
 export(test_configuration)
 export(test_permutation)
 export(test_random)
-importFrom(cli,cli_div)
-importFrom(cli,cli_end)
-importFrom(cli,cli_inform)
-importFrom(manynet,bind_node_attributes)
-importFrom(manynet,generate_configuration)
-importFrom(manynet,generate_random)
-importFrom(manynet,is_complex)
-importFrom(manynet,is_directed)
+importFrom(manynet,
+  bind_node_attributes,
+  generate_configuration,
+  generate_random,
+  is_complex,
+  is_directed,
+  snet_info
+)
+importFrom(netrics,net_by_heterophily)