diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
new file mode 100644
index 0000000..16d18a6
--- /dev/null
+++ b/.github/pull_request_template.md
@@ -0,0 +1,7 @@
+## Pull request (PR) description:
+> Provide a brief description of the PR here.
+> 
+> It does not need to list what each individual commit does, but rather provide a high-level overview of the PR.
+
+## Issues resolved:
+> Any associated issues should be provided here using the format: 'Resolves #<issue>' (e.g. Resolves #1). If there are none, use 'n/a' instead.
diff --git a/.github/workflows/pr-ci-report.yml b/.github/workflows/pr-ci-report.yml
new file mode 100644
index 0000000..1ed6fe6
--- /dev/null
+++ b/.github/workflows/pr-ci-report.yml
@@ -0,0 +1,249 @@
+name: Pull Request CI Report
+
+on:
+  pull_request:
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  python-tests:
+    name: Python ${{ matrix.python-version }} (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    if: github.event.pull_request.head.repo.full_name == github.repository
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.14", "3.15"]
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: OS version (Linux)
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          . /etc/os-release
+          echo "OS_NAME=$NAME" >> "$GITHUB_ENV"
+          echo "OS_VER=$VERSION_ID" >> "$GITHUB_ENV"
+
+      - name: OS version (macOS)
+        if: runner.os == 'macOS'
+        shell: bash
+        run: |
+          echo "OS_NAME=macOS" >> "$GITHUB_ENV"
+          echo "OS_VER=$(sw_vers -productVersion)" >> "$GITHUB_ENV"
+
+      - name: Install Linux Qt runtime dependencies
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libegl1 \
+            libgl1 \
+            libdbus-1-3 \
+            libxkbcommon-x11-0 \
+            libxcb-cursor0 \
+            libxcb-icccm4 \
+            libxcb-image0 \
+            libxcb-keysyms1 \
+            libxcb-randr0 \
+            libxcb-render-util0 \
+            libxcb-shape0 \
+            libxcb-xinerama0 \
+            libxcb-xfixes0 \
+            xvfb
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@ae62891fec2bb8e7d6c99fc78c9fec3a63790f8d
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Sync dependencies
+        run: uv sync --all-extras
+
+      - name: Run pytest
+        id: pytest
+        continue-on-error: true
+        run: uv run pytest
+
+      - name: Build package
+        id: build
+        continue-on-error: true
+        run: uv build
+
+      - name: Add venv bin to PATH
+        shell: bash
+        run: echo "$PWD/.venv/bin" >> "$GITHUB_PATH"
+
+      - name: Check CLI entry point
+        id: cli
+        continue-on-error: true
+        run: comms --help
+
+      - name: Write result file
+        if: always()
+        shell: bash
+        run: |
+          mkdir -p result
+          cat > result/result.json <<EOF
+          {
+            "os_name": "${{ env.OS_NAME }}",
+            "os_ver": "${{ env.OS_VER }}",
+            "python_version": "${{ matrix.python-version }}",
+            "tests": "${{ steps.pytest.outcome == 'success' && 'pass' || 'fail' }}",
+            "build": "${{ steps.build.outcome == 'success' && 'pass' || 'fail' }}",
+            "cli": "${{ steps.cli.outcome == 'success' && 'pass' || 'fail' }}"
+          }
+          EOF
+
+      - name: Upload result artifact
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: python-result-${{ matrix.os }}-${{ matrix.python-version }}
+          path: result/result.json
+
+      - name: Fail if any check failed
+        if: always() && (steps.pytest.outcome == 'failure' || steps.build.outcome == 'failure' || steps.cli.outcome == 'failure')
+        run: exit 1
+
+  r-tests:
+    name: R ${{ matrix.r-version }} (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    if: github.event.pull_request.head.repo.full_name == github.repository
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        r-version: ["4.4.3", "4.5.3", "4.6.1"]
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: OS version (Linux)
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          . /etc/os-release
+          echo "OS_NAME=$NAME" >> "$GITHUB_ENV"
+          echo "OS_VER=$VERSION_ID" >> "$GITHUB_ENV"
+          echo "USE_BUNDLED_LIBUV=1" >> "$GITHUB_ENV"
+
+      - name: OS version (macOS)
+        if: runner.os == 'macOS'
+        shell: bash
+        run: |
+          echo "OS_NAME=macOS" >> "$GITHUB_ENV"
+          echo "OS_VER=$(sw_vers -productVersion)" >> "$GITHUB_ENV"
+
+      - name: Install Linux runtime dependencies
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libcurl4-openssl-dev \
+            libfontconfig1-dev \
+            libfreetype6-dev \
+            libfribidi-dev \
+            libharfbuzz-dev \
+            libjpeg-dev \
+            libpng-dev \
+            libtiff5-dev \
+            libwebp-dev
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r-version }}
+          use-public-rspm: true
+
+      - name: Install R dependencies
+        run: |
+          Rscript -e 'install.packages("testthat", repos = "https://cloud.r-project.org")'
+          Rscript src/comms/r/deps/install_deps.R
+
+      - name: Run R tests
+        id: rtests
+        continue-on-error: true
+        run: Rscript -e 'testthat::test_dir("tests/r")'
+
+      - name: Write result file
+        if: always()
+        shell: bash
+        run: |
+          mkdir -p result
+          cat > result/result.json <<EOF
+          {
+            "os_name": "${{ env.OS_NAME }}",
+            "os_ver": "${{ env.OS_VER }}",
+            "r_version": "${{ matrix.r-version }}",
+            "tests": "${{ steps.rtests.outcome == 'success' && 'pass' || 'fail' }}"
+          }
+          EOF
+
+      - name: Upload result artifact
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: r-result-${{ matrix.os }}-${{ matrix.r-version }}
+          path: result/result.json
+
+      - name: Fail if R tests failed
+        if: always() && steps.rtests.outcome == 'failure'
+        run: exit 1
+
+  all-checks-passed:
+    name: All checks passed
+    needs: [python-tests, r-tests]
+    if: always() && github.event.pull_request.head.repo.full_name == github.repository
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check job results
+        run: |
+          if [ "${{ needs.python-tests.result }}" != "success" ] || \
+             [ "${{ needs.r-tests.result }}" != "success" ]; then
+            echo "One or more required checks failed."
+            exit 1
+          fi
+          echo "All required checks passed."
+
+  summary:
+    name: Post pull request CI report
+    needs: [python-tests, r-tests]
+    if: always() && github.event.pull_request.head.repo.full_name == github.repository
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout branch for workflow script
+        uses: actions/checkout@v7
+
+      - name: Download Python results
+        uses: actions/download-artifact@v7
+        continue-on-error: true
+        with:
+          pattern: python-result-*
+          path: results/python
+
+      - name: Download R results
+        uses: actions/download-artifact@v7
+        continue-on-error: true
+        with:
+          pattern: r-result-*
+          path: results/r
+
+      - name: List all downloaded files
+        shell: bash
+        run: ls -a
+
+      - name: Build summary
+        id: build
+        shell: bash
+        run: python3 .github/workflows/pr_ci_report.py
+
+      - name: Comment on pull request
+        uses: marocchino/sticky-pull-request-comment@v3
+        with:
+          header: pull-request-ci-report
+          path: pr_ci_report.md
\ No newline at end of file
diff --git a/.github/workflows/pr-version-check.yml b/.github/workflows/pr-version-check.yml
new file mode 100644
index 0000000..57514af
--- /dev/null
+++ b/.github/workflows/pr-version-check.yml
@@ -0,0 +1,66 @@
+name: Main Branch Pull Request Version Check
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  version-check:
+    name: Check version bump
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout PR branch
+        uses: actions/checkout@v7
+
+      - name: Read PR version
+        id: pr_version
+        run: |
+          VERSION=$(grep -m1 '^version *= *' pyproject.toml | sed -E 's/version *= *"([^"]+)"/\1/')
+          if [ -z "$VERSION" ]; then
+            echo "Could not read version from pyproject.toml" >&2
+            exit 1
+          fi
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      - name: Read main version
+        id: main_version
+        run: |
+          git fetch origin main --depth=1
+          VERSION=$(git show origin/main:pyproject.toml | grep -m1 '^version *= *' | sed -E 's/version *= *"([^"]+)"/\1/')
+          if [ -z "$VERSION" ]; then
+            echo "Could not read version from main's pyproject.toml" >&2
+            exit 1
+          fi
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@ae62891fec2bb8e7d6c99fc78c9fec3a63790f8d
+
+      - name: Compare versions
+        run: |
+          PR_VERSION="${{ steps.pr_version.outputs.version }}"
+          MAIN_VERSION="${{ steps.main_version.outputs.version }}"
+          echo "PR version: $PR_VERSION"
+          echo "main version: $MAIN_VERSION"
+          uv run --with packaging python3 - "$PR_VERSION" "$MAIN_VERSION" <<'EOF'
+          import sys
+          from packaging.version import Version, InvalidVersion
+
+          pr_raw, main_raw = sys.argv[1], sys.argv[2]
+
+          try:
+              pr = Version(pr_raw)
+              main = Version(main_raw)
+          except InvalidVersion as e:
+              print(f"Could not parse version as PEP 440: {e}", file=sys.stderr)
+              sys.exit(1)
+
+          if pr <= main:
+              print(f'Version in pyproject.toml ({pr_raw}) is not greater than main ({main_raw}). Versions must strictly increase.'', file=sys.stderr)
+              sys.exit(1)
+
+          print(f'OK: {pr_raw} > {main_raw}'')
+          EOF
\ No newline at end of file
diff --git a/.github/workflows/pr_ci_report.py b/.github/workflows/pr_ci_report.py
new file mode 100644
index 0000000..2794014
--- /dev/null
+++ b/.github/workflows/pr_ci_report.py
@@ -0,0 +1,131 @@
+'''
+pr_ci_report.py
+
+Helper script for Pull Request CI Report GitHub Actions workflow
+Ingests JSON artifacts containing job results and produces a markdown document with the generated result comment
+'''
+
+# Import external dependencies
+import glob, json
+
+# Define constant icons for pass/partial pass/fail
+ICON_PASS = '✅'
+ICON_PARTIAL = '⚠️'
+ICON_FAIL = '❌'
+
+# load: given a glob pattern, read all matching JSON files into items and return
+def load(pattern):
+    items = []
+    for f in glob.glob(pattern):
+        with open(f) as fh:
+            items.append(json.load(fh))
+    return items
+
+# os_key: given an item, return the os_name and os_ver variables (for operating system name/version)
+def os_key(item):
+    return (item.get('os_name', 'Unknown'), item.get('os_ver', 'unknown'))
+
+# summary_icon: given passed and total jobs, return a summary icon depending on proportion of passed jobs
+def summary_icon(passed, total):
+    if total == 0:
+        return 'n/a'
+    if passed == total:
+        return ICON_PASS
+    if passed == 0:
+        return ICON_FAIL
+    return ICON_PARTIAL
+
+# load Python and R test results
+py = load("results/python/**/result.json")
+r = load("results/r/**/result.json")
+
+# extract all OS keys and sort in descending order
+os_keys = sorted(set(os_key(i) for i in py) | set(os_key(i) for i in r), reverse=True)
+
+# extract all Python versions and sort in ascending order
+python_versions = sorted(set(i['python_version'] for i in py), reverse=False)
+
+# extract all R versions and sort in ascending order
+r_versions = sorted(set(i['r_version'] for i in r), reverse=False)
+
+
+# build summary comment as list of lines
+lines = []
+lines.append('# Pull Request CI Report')
+
+# add caution alert about Crux/TRFP tests to comment
+lines.append('')
+lines.append('> [!CAUTION]')
+lines.append('> GitHub Actions runners do not have ThermoRawFileParser or Crux installed. Tests dependent on these binaries are skipped and should instead be run manually before merging.')
+
+# add summary to comment
+lines.append('')
+lines.append('<br>')
+lines.append('')
+lines.append('## Summary')
+lines.append('')
+lines.append('Operating System | Source distributions built? | CLI available? | Passed Python tests? | Passed R tests?')
+lines.append('--|--|--|--|--')
+for name, ver in os_keys:
+    py_cells = [i for i in py if os_key(i) == (name, ver)]
+    r_cells = [i for i in r if os_key(i) == (name, ver)]
+    build_ok = len(py_cells) > 0 and all(c['build'] == 'pass' for c in py_cells)
+    cli_ok = len(py_cells) > 0 and all(c['cli'] == 'pass' for c in py_cells)
+    py_passed = sum(1 for c in py_cells if c['tests'] == 'pass')
+    r_passed = sum(1 for c in r_cells if c['tests'] == 'pass')
+    build_icon = ICON_PASS if build_ok else ICON_FAIL
+    cli_icon = ICON_PASS if cli_ok else ICON_FAIL
+    lines.append(f'{name} ({ver}) | {build_icon} | {cli_icon} | {summary_icon(py_passed, len(py_cells))} | {summary_icon(r_passed, len(r_cells))}')
+
+# add Python test results to comment
+lines.append('')
+lines.append('<br>')
+lines.append('')
+lines.append('## Python Tests')
+lines.append('')
+lines.append(f'Python versions tested: {", ".join(python_versions) if python_versions else "none"}')
+if python_versions:
+    lines.append('')
+    lines.append(' Operating System | ' + ' | '.join(f'Python {v}' for v in python_versions))
+    lines.append('-- |' * (len(python_versions) + 1))
+    for name, ver in os_keys:
+        row = [f'{name} ({ver})']
+        for v in python_versions:
+            match = next(
+                (result for result in py if os_key(result) == (name, ver) and result['python_version'] == v),
+                None,
+            )
+            row.append('n/a' if match is None else (ICON_PASS if match['tests'] == 'pass' else ICON_FAIL))
+        lines.append(' | '.join(row))
+
+# add R test results to comment
+lines.append('')
+lines.append('<br>')
+lines.append('')
+lines.append('## R Tests')
+lines.append('')
+lines.append(f'R versions tested: {", ".join(r_versions) if r_versions else "none"}')
+if r_versions:
+    lines.append('')
+    lines.append(' Operating System | ' + ' | '.join(f'R {v}' for v in r_versions))
+    lines.append('-- |' * (len(r_versions) + 1))
+    for name, ver in os_keys:
+        row = [f'{name} ({ver})']
+        for v in r_versions:
+            match = next(
+                (result for result in r if os_key(result) == (name, ver) and result['r_version'] == v),
+                None,
+            )
+            row.append('n/a' if match is None else (ICON_PASS if match['tests'] == 'pass' else ICON_FAIL))
+        lines.append(' | '.join(row))
+
+# add footer to comment
+lines.append('')
+lines.append('<br>')
+lines.append('')
+lines.append('---')
+lines.append('_Auto-generated by the comMS Pull Request CI Report workflow. See full logs in the Actions run for this PR._')
+
+# write comment to markdown file
+with open('pr_ci_report.md', 'w') as f:
+    f.write('\n'.join(lines))
\ No newline at end of file
diff --git a/.github/workflows/publish-release.yml b/.github/workflows/publish-release.yml
new file mode 100644
index 0000000..126d199
--- /dev/null
+++ b/.github/workflows/publish-release.yml
@@ -0,0 +1,40 @@
+name: Create comMS Release
+
+on:
+  push:
+    branches: [main]
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    name: Build and publish release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@ae62891fec2bb8e7d6c99fc78c9fec3a63790f8d
+
+      - name: Read version
+        id: version
+        run: |
+          VERSION=$(grep -m1 '^version *= *' pyproject.toml | sed -E 's/version *= *"([^"]+)"/\1/')
+          if [ -z "$VERSION" ]; then
+            echo "Could not read version from pyproject.toml" >&2
+            exit 1
+          fi
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish release
+        uses: softprops/action-gh-release@v3
+        with:
+          tag_name: v${{ steps.version.outputs.version }}
+          name: v${{ steps.version.outputs.version }}
+          generate_release_notes: true
+          draft: false
+          files: dist/*
\ No newline at end of file
diff --git a/README.md b/README.md
index 484ee66..c251cf7 100644
--- a/README.md
+++ b/README.md
@@ -43,7 +43,7 @@ Tool | Minimum version | Purpose | Platform notes
 [ThermoRawFileParser][trfp-url] | 1.4.5 | `.RAW` → `.mzML` conversion | Versions < 2.0.0 require [Mono](https://mono-project.com) on Linux/macOS
 
 ### `comms report` dependencies
-The `report` command requires R (≥ 4.3.0) and a set of R packages (listed in the [report command documentation](./docs/commands.md#the-report-command)). Check or install the required R packages with:
+The `report` command requires R (≥ 4.4.0) and a set of R packages (listed in the [report command documentation](./docs/commands.md#the-report-command)). Check or install the required R packages with:
 ```bash
 comms r-utils check
 comms r-utils install
diff --git a/tests/r/test_utils_import.R b/tests/r/test_utils_import.R
index ce81684..c52881a 100644
--- a/tests/r/test_utils_import.R
+++ b/tests/r/test_utils_import.R
@@ -25,11 +25,11 @@ make_cont_csv <- function(tmp_dir) {
   path <- file.path(tmp_dir, "cont.csv")
   write_csv(tibble(protein.id="CONT001", protein.annotation="Keratin", protein.reason="skin"), path); path
 }
-make_sc_file <- function(tmp_dir, filename="s1.spectral-counts.target.txt") {
+make_sc_file <- function(tmp_dir, filename="s1_dNSAF.spectral-counts.target.txt") {
   path <- file.path(tmp_dir, filename)
   write_tsv(tibble(
-    proteinId = c("Mtrun001", "Mtrun002", "CONT001"),
-    dNSAF = c(0.6, 0.4, 0.1)
+    "protein id" = c("Mtrun001", "Mtrun002", "CONT001"),
+    "dNSAF" = c(0.6, 0.4, 0.1)
   ), path)
   path
 }
@@ -92,8 +92,8 @@ test_that("loadSpectralCounts retains dNSAF column", {
 test_that("mergeResults produces a wide tibble with one dNSAF column per sample", {
   ref  <- loadRefInfo(make_ref_info(tmp))
   cont <- loadContInfo(make_cont_csv(tmp))
-  s1 <- make_sc_file(tmp, "s1.spectral-counts.target.txt")
-  s2 <- make_sc_file(tmp, "s2.spectral-counts.target.txt")
+  s1 <- make_sc_file(tmp, "s1_dNSAF.spectral-counts.target.txt")
+  s2 <- make_sc_file(tmp, "s2_dNSAF.spectral-counts.target.txt")
   result <- mergeResults(list(
     s1=loadSpectralCounts(s1, ref, cont),
     s2=loadSpectralCounts(s2, ref, cont)
@@ -106,7 +106,7 @@ test_that("mergeResults preserves proteinId and proteinAnnotation columns", {
   ref  <- loadRefInfo(make_ref_info(tmp))
   cont <- loadContInfo(make_cont_csv(tmp))
   result <- mergeResults(list(
-    s1=loadSpectralCounts(make_sc_file(tmp, "s1.spectral-counts.target.txt"), ref, cont)
+    s1=loadSpectralCounts(make_sc_file(tmp, "s1_dNSAF.spectral-counts.target.txt"), ref, cont)
   ))
   expect_true(all(c("proteinId", "proteinAnnotation") %in% colnames(result)))
 })
@@ -114,13 +114,13 @@ test_that("mergeResults preserves proteinId and proteinAnnotation columns", {
 test_that("mergeResults fills absent proteins with 0 rather than NA", {
   ref <- loadRefInfo(make_ref_info(tmp))
   cont <- loadContInfo(make_cont_csv(tmp))
-  s2_path <- file.path(tmp, "s2_partial.spectral-counts.target.txt")
+  s2_path <- file.path(tmp, "s2.partial_dNSAF.spectral-counts.target.txt")
   write_tsv(tibble(
-    proteinId = "Mtrun001",
-    dNSAF = 1.0
+    `protein id` = "Mtrun001",
+    `dNSAF` = 1.0
   ), s2_path)
   result <- mergeResults(list(
-    s1=loadSpectralCounts(make_sc_file(tmp, "s1.spectral-counts.target.txt"), ref, cont),
+    s1=loadSpectralCounts(make_sc_file(tmp, "s1_dNSAF.spectral-counts.target.txt"), ref, cont),
     s2=loadSpectralCounts(s2_path, ref, cont)
   ))
   mtrun002_s2 <- result[result$proteinId == "Mtrun002", "dNSAF_s2"][[1]]