From 5c3557e9b04c8364c4fbab367c91462d06d01d12 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 13:53:50 +0200
Subject: [PATCH 01/18] ci(py): add maturin workflow

---
 .github/workflows/maturin.yaml | 169 +++++++++++++++++++++++++++++++++
 1 file changed, 169 insertions(+)
 create mode 100644 .github/workflows/maturin.yaml

diff --git a/.github/workflows/maturin.yaml b/.github/workflows/maturin.yaml
new file mode 100644
index 0000000..be7c696
--- /dev/null
+++ b/.github/workflows/maturin.yaml
@@ -0,0 +1,169 @@
+# This file is autogenerated by maturin v1.7.0
+# To update, run
+#
+#    maturin generate-ci github -m pyfuzon/Cargo.toml
+#
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+          - runner: ubuntu-latest
+            target: s390x
+          - runner: ubuntu-latest
+            target: ppc64le
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path pyfuzon/Cargo.toml
+          sccache: 'true'
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path pyfuzon/Cargo.toml
+          sccache: 'true'
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path pyfuzon/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-12
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path pyfuzon/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist --manifest-path pyfuzon/Cargo.toml
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: "startsWith(github.ref, 'refs/tags/')"
+    needs: [linux, musllinux, windows, macos, sdist]
+    steps:
+      - uses: actions/download-artifact@v4
+      - name: Publish to PyPI
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

From 1357d58230af320f321bf529299010c2ee9aab80 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 14:53:33 +0200
Subject: [PATCH 02/18] ci(py): drop windows build, as rff is unix-only

---
 .github/workflows/maturin.yaml | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/.github/workflows/maturin.yaml b/.github/workflows/maturin.yaml
index be7c696..3b7c370 100644
--- a/.github/workflows/maturin.yaml
+++ b/.github/workflows/maturin.yaml
@@ -85,33 +85,6 @@ jobs:
           name: wheels-musllinux-${{ matrix.platform.target }}
           path: dist
 
-  windows:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: windows-latest
-            target: x64
-          - runner: windows-latest
-            target: x86
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-          architecture: ${{ matrix.platform.target }}
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --manifest-path pyfuzon/Cargo.toml
-          sccache: 'true'
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-windows-${{ matrix.platform.target }}
-          path: dist
-
   macos:
     runs-on: ${{ matrix.platform.runner }}
     strategy:

From 3c29ed5ba4b511bb13f844c9647dbf371b8f2759 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 15:06:07 +0200
Subject: [PATCH 03/18] ci(py): drop windows job dep

---
 .github/workflows/maturin.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/maturin.yaml b/.github/workflows/maturin.yaml
index 3b7c370..8bf94d0 100644
--- a/.github/workflows/maturin.yaml
+++ b/.github/workflows/maturin.yaml
@@ -130,7 +130,7 @@ jobs:
     name: Release
     runs-on: ubuntu-latest
     if: "startsWith(github.ref, 'refs/tags/')"
-    needs: [linux, musllinux, windows, macos, sdist]
+    needs: [linux, musllinux, macos, sdist]
     steps:
       - uses: actions/download-artifact@v4
       - name: Publish to PyPI

From 26ae574ec299958188f8c6ff03d2277344e936e9 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 15:11:48 +0200
Subject: [PATCH 04/18] docs: contrib guide

---
 CONTRIBUTING.md | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..199a490
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,37 @@
+# Contributing
+
+**Thank you very much for considering contributing to this project!**
+
+We welcome any form of contribution:
+
+- New Issues (feature requests, bug reports, questions, ideas, ...)
+- Pull Requests (documentation improvements, code improvements, new features,
+  ...)
+
+**Note**: Before you take the time to open a pull request, please open an issue
+first. This will give us the chance to discuss any potential changes first.
+
+## Opening a Pull Request
+
+Pull requests are the best way to propose changes to the codebase. We actively
+welcome your pull requests:
+
+1. Fork the repo and create your branch from `main`.
+2. If you've added code that should be tested, add tests.
+3. If you've changed APIs, update the documentation.
+4. Ensure the test suite passes: the CI will help you.
+5. Create the pull request.
+
+**Note:** Pull-requests can only be merged if the CI passes.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under this
+[license](LICENSE).
+
+## Important Links
+
+- [Open Issues](https://github.com/sdsc-ordes/fuzon/issues)
+- [Open Pull Requests](https://github.com/sdsc-ordes/fuzon/pulls)
+- [Development Section in the README](https://github.com/sdsc-ordes/fuzon#development)
+- [LICENSE](https://github.com/sdsc-ordes/fuzon/blob/main/LICENSE)

From 8822485c7fa9a4916fee055d0c3037a7f53ea3bb Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 15:12:49 +0200
Subject: [PATCH 05/18] chore: generic config files

---
 .editorconfig       |  17 +++++++
 .gitattributes      | 106 ++++++++++++++++++++++++++++++++++++++++++++
 .prettierrc         |   9 ++++
 rust-toolchain.toml |   4 ++
 rustfmt.toml        |   3 ++
 5 files changed, 139 insertions(+)
 create mode 100644 .editorconfig
 create mode 100644 .gitattributes
 create mode 100644 .prettierrc
 create mode 100644 rust-toolchain.toml
 create mode 100644 rustfmt.toml

diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..004129e
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,17 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 4
+
+[*.{json,yaml,yml}]
+indent_size = 2
+
+[*.nix]
+indent_size = 2
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..11eaeb2
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,106 @@
+
+# Attribute file for assigning key=value pairs to paths.
+# Any edit to this file needs to be reviewed by admins.
+# These attributes define among other things
+# which files are transferred into Git LFS when
+# staging/commiting.
+#
+# Please read the docs first: https://git-scm.com/docs/gitattributes
+#
+# Restrictions:
+#  - No backslashes for paths! (also on Windows)
+#  - For spaces in paths use `[[:space:]]`.
+#
+
+# Overall LF lineendings for the
+# following files.
+# ===============================
+* text=auto eol=lf
+
+# Default attribute patterns for common binary files
+# which should be stored in Git LFS.
+# ==================================================
+# Images
+*.[Ii][Cc][Oo] filter=lfs diff=lfs merge=lfs -text
+*.[Jj][Pp][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Jj][Pp][Ee][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Pp][Nn][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Gg][Ii][Ff] filter=lfs diff=lfs merge=lfs -text
+*.[Tt][Ii][Ff] filter=lfs diff=lfs merge=lfs -text
+*.[Tt][Ii][Ff][Ff] filter=lfs diff=lfs merge=lfs -text
+*.[Pp][Ss][Dd] filter=lfs diff=lfs merge=lfs -text
+*.[Aa][Ii] filter=lfs diff=lfs merge=lfs -text
+
+# Media
+*.[Pp][Dd][Ff] filter=lfs diff=lfs merge=lfs -text
+
+# Video/Audio
+*.[Mm][Oo][Vv] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp]4 filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp]2 filter=lfs diff=lfs merge=lfs -text
+*.[Mm]4[Vv] filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Mm][Vv] filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Mm][Vv] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp][Ee] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp][Ee][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Aa][Vv][Ii] filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Ee][Bb][Mm] filter=lfs diff=lfs merge=lfs -text
+*.[Oo][Gg][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp]3 filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Aa][Vv] filter=lfs diff=lfs merge=lfs -text
+
+# MS Office
+*.[Dd][Oo][Cc] filter=lfs diff=lfs merge=lfs -text
+*.[Dd][Oo][Cc][Xx] filter=lfs diff=lfs merge=lfs -text
+*.[Pp][Pp][Tt] filter=lfs diff=lfs merge=lfs -text
+*.[Pp][Pp][Tt][Xx] filter=lfs diff=lfs merge=lfs -text
+*.[Xx][Ll][Ss] filter=lfs diff=lfs merge=lfs -text
+*.[Xx][Ll][Ss][Xx] filter=lfs diff=lfs merge=lfs -text
+*.[Dd][Oo][Tt][Xx] filter=lfs diff=lfs merge=lfs -text
+
+# Fonts
+*.[Tt][Tt][Ff] filter=lfs diff=lfs merge=lfs -text
+*.[Oo][Tt][Ff] filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Oo][Ff][Ff] filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Oo][Ff][Ff]2 filter=lfs diff=lfs merge=lfs -text
+
+# Data Zips
+*.[Zz][Ii][Pp] filter=lfs diff=lfs merge=lfs -text
+*.[Zz] filter=lfs diff=lfs merge=lfs -text
+*.[Gg][Zz] filter=lfs diff=lfs merge=lfs -text
+*.[Tt][Aa][Rr] filter=lfs diff=lfs merge=lfs -text
+*.[Tt][Gg][Zz] filter=lfs diff=lfs merge=lfs -text
+*.[Zz][Ii][Pp] filter=lfs diff=lfs merge=lfs -text
+*.[Bb][Zz]2 filter=lfs diff=lfs merge=lfs -text
+*.[Ll][Zz][Mm][Aa] filter=lfs diff=lfs merge=lfs -text
+*.[Ll][Zz] filter=lfs diff=lfs merge=lfs -text
+*.[Ll][Zz]4 filter=lfs diff=lfs merge=lfs -text
+*.7[Zz] filter=lfs diff=lfs merge=lfs -text
+*.[Ss]7[Zz] filter=lfs diff=lfs merge=lfs -text
+*.[Rr][Aa][Rr] filter=lfs diff=lfs merge=lfs -text
+*.[Bb][Zz][Ii][Pp] filter=lfs diff=lfs merge=lfs -text
+
+# Packages
+*.[Xx][Pp][Ii] filter=lfs diff=lfs merge=lfs -text
+*.[Dd][Mm][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Ii][Mm][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Ii][Ss][Oo] filter=lfs diff=lfs merge=lfs -text
+*.[Ww][Ii][Mm] filter=lfs diff=lfs merge=lfs -text
+*.[Ss][Ww][Mm] filter=lfs diff=lfs merge=lfs -text
+*.[Ee][Ss][Dd] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Ss][Ii] filter=lfs diff=lfs merge=lfs -text
+*.[Pp][Kk][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Mm][Pp][Kk][Gg] filter=lfs diff=lfs merge=lfs -text
+*.[Dd][Ee][Bb] filter=lfs diff=lfs merge=lfs -text
+*.[Rr][Pp][Mm] filter=lfs diff=lfs merge=lfs -text
+*.[Jj][Aa][Rr] filter=lfs diff=lfs merge=lfs -text
+
+# Libraries
+*.[Pp][Dd][Bb] filter=lfs diff=lfs merge=lfs -text
+*.[Dd][Ll][Ll] filter=lfs diff=lfs merge=lfs -text
+*.[Ll][Ii][Bb] filter=lfs diff=lfs merge=lfs -text
+
+# General binary
+*.[Bb][Ii][Nn] filter=lfs diff=lfs merge=lfs -text
+*.[Ee][Xx][Ee] filter=lfs diff=lfs merge=lfs -text
diff --git a/.prettierrc b/.prettierrc
new file mode 100644
index 0000000..e480fd5
--- /dev/null
+++ b/.prettierrc
@@ -0,0 +1,9 @@
+{
+  "printWidth": 80,
+  "tabWidth": 2,
+  "semi": false,
+  "singleQuote": false,
+  "overrides": [
+    { "files": "*.md", "options": { "proseWrap": "always", "tabWidth": 2 } }
+  ]
+}
diff --git a/rust-toolchain.toml b/rust-toolchain.toml
new file mode 100644
index 0000000..782c141
--- /dev/null
+++ b/rust-toolchain.toml
@@ -0,0 +1,4 @@
+[toolchain]
+channel = "nightly-2024-06-17"
+components = [ "rustfmt", "rust-analyzer", "miri", "rust-docs", "clippy", "rust-src"]
+profile = "default"
diff --git a/rustfmt.toml b/rustfmt.toml
new file mode 100644
index 0000000..9aeb106
--- /dev/null
+++ b/rustfmt.toml
@@ -0,0 +1,3 @@
+edition = "2021"
+reorder_imports = true
+imports_granularity = "Crate"

From cc817ea45739ea6f5a3fb6654ed95178d8eafadf Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 16:08:32 +0200
Subject: [PATCH 06/18] chore: add nix-based tooling

---
 .envrc                            |   1 +
 tools/bench/benchmark.sh          | 171 ++++++++++++++++++++++++++++++
 tools/build-image.sh              |  68 ++++++++++++
 tools/build-package.sh            |  19 ++++
 tools/ci/assert-tag.sh            |  67 ++++++++++++
 tools/ci/create-github-release.sh |  27 +++++
 tools/ci/images/Containerfile     |  43 ++++++++
 tools/ci/setup-git.sh             |  15 +++
 tools/ci/upload-ci-images.sh      |  41 +++++++
 tools/ci/upload-image.sh          |  52 +++++++++
 tools/format-rust.sh              |  22 ++++
 tools/general.sh                  | 108 +++++++++++++++++++
 tools/lint-rust.sh                |  22 ++++
 tools/lint-ub-rust.sh             |  18 ++++
 tools/nix/flake.nix               | 144 +++++++++++++++++++++++++
 tools/nix/images/ci.nix           |  22 ++++
 tools/nix/images/fuzon.nix        |  30 ++++++
 tools/nix/pkgs/fuzon.nix          |  32 ++++++
 tools/release.sh                  | 132 +++++++++++++++++++++++
 19 files changed, 1034 insertions(+)
 create mode 100644 .envrc
 create mode 100644 tools/bench/benchmark.sh
 create mode 100755 tools/build-image.sh
 create mode 100755 tools/build-package.sh
 create mode 100755 tools/ci/assert-tag.sh
 create mode 100755 tools/ci/create-github-release.sh
 create mode 100644 tools/ci/images/Containerfile
 create mode 100755 tools/ci/setup-git.sh
 create mode 100755 tools/ci/upload-ci-images.sh
 create mode 100755 tools/ci/upload-image.sh
 create mode 100755 tools/format-rust.sh
 create mode 100755 tools/general.sh
 create mode 100755 tools/lint-rust.sh
 create mode 100755 tools/lint-ub-rust.sh
 create mode 100644 tools/nix/flake.nix
 create mode 100644 tools/nix/images/ci.nix
 create mode 100644 tools/nix/images/fuzon.nix
 create mode 100644 tools/nix/pkgs/fuzon.nix
 create mode 100755 tools/release.sh

diff --git a/.envrc b/.envrc
new file mode 100644
index 0000000..b4232c4
--- /dev/null
+++ b/.envrc
@@ -0,0 +1 @@
+use flake ./tools/nix#default
diff --git a/tools/bench/benchmark.sh b/tools/bench/benchmark.sh
new file mode 100644
index 0000000..30db925
--- /dev/null
+++ b/tools/bench/benchmark.sh
@@ -0,0 +1,171 @@
+#!/usr/bin/env bash
+
+# Benchmark runtime and memory usage of tripsu
+# Compares the working directory version against a baseline branch (main by default)
+
+set -euo pipefail
+
+### Final output path
+OUTPUT="profiling.md"
+PROFILE='release'
+BUILD_ARGS=( )
+[[ "${PROFILE}" == 'release' ]] && BUILD_ARGS+=( '--release' )
+### setup binaries
+
+# baseline binary
+BASE_BRANCH='main'
+
+BASE_DIR=$(mktemp -d)
+BASE_URL="$(git config --get remote.origin.url)"
+(
+    GIT_CLONE_PROTECTION_ACTIVE=false \
+    git clone \
+        --branch "${BASE_BRANCH}" \
+        "${BASE_URL}" \
+        "${BASE_DIR}" \
+    && cd "${BASE_DIR}" \
+    && just build "${BUILD_ARGS[@]}"
+)
+BASE_BIN="${BASE_DIR}/target/${PROFILE}/tripsu"
+
+# current binary
+COMP_BRANCH="$(git rev-parse --abbrev-ref HEAD)"
+just build "${BUILD_ARGS[@]}"
+COMP_BIN="./target/${PROFILE}/tripsu"
+
+# setup data
+DATA_URL="https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/proteomes.rdf.xz"
+INPUT="/tmp/proteomes.nt"
+
+# Download data if needed
+if [ ! -f ${INPUT} ]; then
+    curl "${DATA_URL}" \
+    | xz -dc -  \
+    | rdfpipe-rs -i rdf-xml -o nt - \
+    > "${INPUT}" || rm "${INPUT}"
+fi
+
+# setup config
+RULES=$(mktemp)
+BASE_IDX=$(mktemp)
+COMP_IDX=$(mktemp)
+
+cat << EOF > "${RULES}"
+
+nodes:
+  of_type:
+    - "http://purl.uniprot.org/core/Proteome"
+    - "http://purl.uniprot.org/core/Strain"
+
+objects:
+  on_type_predicate:
+    "http://purl.uniprot.org/core/Submission_Citation":
+      - "http://purl.uniprot.org/core/author"
+  
+  on_predicate:
+    - "http://purl.org/dc/terms/identifier"
+
+EOF
+
+### Commands to benchmark
+BASE_CMD_IDX="${BASE_BIN} index -o ${BASE_IDX} ${INPUT}"
+COMP_CMD_IDX="${COMP_BIN} index -o ${COMP_IDX} ${INPUT}"
+BASE_CMD_PSD="${BASE_BIN} pseudo -r ${RULES} -x ${BASE_IDX} ${INPUT}"
+COMP_CMD_PSD="${COMP_BIN} pseudo -r ${RULES} -x ${COMP_IDX} ${INPUT}"
+
+### functions for profiling
+
+cpu_prof() {
+    local branch1=$1
+    local cmd1=$2
+    local branch2=$3
+    local cmd2=$4
+    local out=$5
+    hyperfine --export-markdown "${out}" -r 5 \
+        -n "${branch1}" "${cmd1}" \
+        -n "${branch2}" "${cmd2}"
+}
+
+mem_prof() {
+    local name=$1
+    local cmd=$2
+    local heap_out
+    heap_out=$(mktemp)
+    echo -n "$name: "
+    # shellcheck disable=SC2086
+    heaptrack -o "${heap_out}" ${cmd} >/dev/null
+    heaptrack_print "${heap_out}.zst" \
+    | grep '^peak heap memory'
+}
+
+make_report() {
+    local cpu_index=$1
+    local cpu_pseudo=$2
+    local mem_index=$3
+    local mem_pseudo=$4
+    local base_branch=$5
+
+    cat <<-MD
+	# tripsu profiling
+
+	> date: $(date -u +%Y-%m-%d)
+
+    Comparing $(git branch --show-current) against $base_branch.
+	
+	## Timings
+	
+	Run time compared using hyperfine
+	
+	### Indexing
+	
+	$(cat "${cpu_index}")
+	
+	### Pseudonymization
+	
+	$(cat "${cpu_pseudo}")
+	
+	## Memory
+	
+	Heap memory usage compared using heaptrack
+	
+	### Indexing
+	
+	$(cat "${mem_index}")
+	
+	### Pseudonymization
+	
+	$(cat "${mem_pseudo}")
+	MD
+}
+
+
+###  Run profiling
+
+## Profile cpu time
+HYPF_IDX_OUT=$(mktemp)
+HYPF_PSD_OUT=$(mktemp)
+
+# indexing
+cpu_prof "${BASE_BRANCH}" "${BASE_CMD_IDX}" \
+         "${COMP_BRANCH}" "${COMP_CMD_IDX}" "${HYPF_IDX_OUT}"
+# pseudonymization
+cpu_prof "${BASE_BRANCH}" "${BASE_CMD_IDX}" \
+         "${COMP_BRANCH}" "${COMP_CMD_IDX}" "${HYPF_PSD_OUT}"
+
+## Profile memory
+HEAP_IDX_OUT=$(mktemp)
+HEAP_PSD_OUT=$(mktemp)
+
+# indexing
+mem_prof "${BASE_BRANCH}" "${BASE_CMD_IDX}" >  "${HEAP_IDX_OUT}"
+mem_prof "${COMP_BRANCH}" "${COMP_CMD_IDX}" >> "${HEAP_IDX_OUT}"
+# pseudonymization
+mem_prof "${BASE_BRANCH}" "${BASE_CMD_PSD}" >  "${HEAP_PSD_OUT}"
+mem_prof "${COMP_BRANCH}" "${COMP_CMD_PSD}" >> "${HEAP_PSD_OUT}"
+
+
+### Reporting
+make_report \
+    "${HYPF_IDX_OUT}" "${HYPF_PSD_OUT}" \
+    "${HEAP_IDX_OUT}" "${HEAP_PSD_OUT}" \
+    "${BASE_BRANCH}" > "${OUTPUT}"
diff --git a/tools/build-image.sh b/tools/build-image.sh
new file mode 100755
index 0000000..11459c7
--- /dev/null
+++ b/tools/build-image.sh
@@ -0,0 +1,68 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+#
+# Build the Nix container image.
+
+set -euo pipefail
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+VERSION_FILE="$ROOT_DIR/Cargo.toml"
+
+function clean_up() {
+    if ! ci_is_running; then
+        # Never change the version file, only
+        # on explicit `just release`.
+        print_info "Restoring '$VERSION_FILE'."
+        git restore "$VERSION_FILE" || true
+    fi
+}
+
+trap clean_up EXIT
+
+function main() {
+    args=("$@")
+
+    if ! ci_is_running || ! ci_is_release; then
+        print_info "Building image for development."
+
+        # Define the image version from Git SHA
+        version="0.0.0-dev.$(git rev-parse --short=7 HEAD)"
+
+        # Write the temporary version file (gets restored...)
+        dasel put -r toml -f "$VERSION_FILE" -t string -v "$version" .package.version
+    else
+        print_info "Building image for release."
+
+        # When CI and in Release, the requested version must match.
+        version=$(dasel -r toml -f "$VERSION_FILE" .package.version -w yaml)
+
+        release_version=${GITHUB_REF##*prepare-v}
+
+        if [ "$version" != "$release_version" ]; then
+            die "The version '$version' in '$VERSION_FILE' does not corresponds" \
+                "with the version '$release_version' to build." \
+                "Update the version file to align!" \
+                "Nix is pure and cannot rely on Git tags to" \
+                "get the version from."
+        fi
+    fi
+
+    image_name=$(nix eval --raw "./tools/nix#images.tripsu.imageName")
+    image_tag=$(nix eval --raw "./tools/nix#images.tripsu.imageTag")
+
+    # We cannot use `:` before the tag, because `skopeo`
+    # is unable to read this path correctly, because it
+    # stupidly deals with it.
+    dir="build/image/$image_name|$image_tag.tar.gz"
+
+    cd "$ROOT_DIR"
+
+    print_info "Building image '$dir'."
+    nix --version
+    nix build -L "./tools/nix#images.tripsu" \
+        --out-link "$dir" "${args[@]}"
+}
+
+main "$@"
diff --git a/tools/build-package.sh b/tools/build-package.sh
new file mode 100755
index 0000000..3d9d1c1
--- /dev/null
+++ b/tools/build-package.sh
@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+#
+# Build the Nix container image.
+
+set -euo pipefail
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+dir="build/package"
+
+print_info "Building the package."
+nix --version
+nix build -L "./tools/nix#tripsu" \
+    --out-link "$dir" \
+    "$@"
diff --git a/tools/ci/assert-tag.sh b/tools/ci/assert-tag.sh
new file mode 100755
index 0000000..16c8872
--- /dev/null
+++ b/tools/ci/assert-tag.sh
@@ -0,0 +1,67 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+#
+# Assert that the release tag exists
+# and check that its on main.
+# On `--push` do push the tag.
+
+set -euo pipefail
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+RELEASE_BRANCH="main"
+
+function main() {
+    local type="$1"
+    local prepare_tag="$2"
+
+    local release_tag=${prepare_tag##*prepare-}
+
+    if [ "$type" = "push" ]; then
+        print_info "Pushing tag '$release_tag'."
+
+        git push origin "$release_tag" ||
+            die "Could not push tag."
+
+    elif [ "$type" = "create-and-check" ]; then
+
+        print_info "Create tag '$release_tag' and check."
+
+        # Gets the message on the annotated commit:
+        deref() {
+            git for-each-ref "refs/tags/$release_tag" --format="%($1)"
+        }
+
+        deref contents
+
+        # Creates a new tag with the same message,
+        # including trailing headers.
+        git tag -a -m "$(deref contents)" "$release_tag" ||
+            die "Could not create tag."
+
+        # Fetch the branch.
+        git fetch --depth 50 origin "$RELEASE_BRANCH"
+
+        # Check if its reachable.
+        if [ -z "$(git rev-list --first-parent \
+            --ancestry-path \
+            "$release_tag^..origin/$RELEASE_BRANCH")" ]; then
+            git log --oneline --graph "$RELEASE_BRANCH" "$release_tag" || true
+            die "Tag is not reachable from '$RELEASE_BRANCH' (--first-parent) !"
+        fi
+
+    elif [ "$type" = "cleanup" ]; then
+
+        print_info "Cleanup the prepare tag."
+        git tag -d "$prepare_tag" || true
+        git push origin :"$prepare_tag" || true
+
+    else
+        die "Type '$type' is not known."
+    fi
+}
+
+main "$@"
diff --git a/tools/ci/create-github-release.sh b/tools/ci/create-github-release.sh
new file mode 100755
index 0000000..2c0102c
--- /dev/null
+++ b/tools/ci/create-github-release.sh
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+# This script is sourced in each step.
+set -u
+set -e
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+function main() {
+    local prepare_tag="$1"
+    local repo="$2"
+
+    local tag=${prepare_tag#prepare-}
+    local version=${tag#v}
+
+    print_info "Creating Github release ... "
+
+    gh release create "$tag" \
+        --repo="$repo" \
+        --title="tripsu: $version" \
+        --generate-notes
+
+    print_info "Successfully created release. All done."
+}
+
+main "$@"
diff --git a/tools/ci/images/Containerfile b/tools/ci/images/Containerfile
new file mode 100644
index 0000000..27c23cf
--- /dev/null
+++ b/tools/ci/images/Containerfile
@@ -0,0 +1,43 @@
+# This is a docker image containing docker and a Nix store.
+# This enables to either run Docker images inside this one,
+# or use `nix develop` to start a sandboxed environment to
+# do other non-docker related stuff.
+
+FROM alpine:latest as base-podman
+LABEL org.opencontainers.image.source https://github.com/sdsc-ordes/tripsu
+LABEL org.opencontainers.image.description "CI container image for tripsu"
+LABEL org.opencontainers.image.license "Apache"
+
+RUN apk add findutils coreutils git jq curl bash just parallel podman
+
+# Nix Image
+# ===============================================
+FROM base-podman as ci-nix
+ARG USER_NAME=ci
+ARG USER_UID=1000
+ARG USER_GID=1000
+ARG CACHE_TOOLCHAIN=false
+ARG USER_HOME="/github/home"
+
+RUN [ "TARGETPLATFORM" = "linux/amd64" ] || echo "Platform not yet supported."
+COPY ./tools /container-setup/tools
+
+# Install Nix and pre-cache the env.
+RUN bash -c ". /container-setup/tools/general.sh && ci_setup_nix"
+
+# Create user (does not work because action/checkout uses `root` in its own container ... 💩)
+# Leave this code here for a reference:
+# RUN mkdir -p "$USER_HOME" && \
+#     adduser "$USER_NAME" -s /bin/zsh -D -u "$USER_UID" -g "$USER_GID" -h "$USER_HOME/$USER_NAME" && \
+#     mkdir -p /etc/sudoers.d && \
+#     echo "$USER_NAME ALL=(root) NOPASSWD:ALL" > "/etc/sudoers.d/$USER_NAME" && \
+#     chmod 0440 "/etc/sudoers.d/$USER_NAME" && \
+#     chown -R "$USER_NAME:$USER_NAME" /home /container-setup
+# USER "$USER_NAME"
+
+COPY rust-toolchain.toml /container-setup/
+RUN [ "${CACHE_TOOLCHAIN}" = "false" ] || { cd /container-setup && \
+    git init && git add . && \
+    nix --accept-flake-config \
+    build --no-link "./tools/nix#devShells.x86_64-linux.ci" && \
+    nix store optimise; }
diff --git a/tools/ci/setup-git.sh b/tools/ci/setup-git.sh
new file mode 100755
index 0000000..2b325c2
--- /dev/null
+++ b/tools/ci/setup-git.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+# This script is sourced in each step.
+set -u
+set -e
+
+git config --global safe.directory "*" || {
+    echo "Could not overwrite safe.directory in Git config." >&2
+    exit 1
+}
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+ci_setup_git
diff --git a/tools/ci/upload-ci-images.sh b/tools/ci/upload-ci-images.sh
new file mode 100755
index 0000000..d67d092
--- /dev/null
+++ b/tools/ci/upload-ci-images.sh
@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+set -e
+set -u
+
+DIR=$(cd -- "$(dirname -- "$0")" &>/dev/null && pwd)
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+function build_ci_image() {
+    local image_type="$1"
+    local repository="$2"
+    local version="$3"
+    local tag="$image_type-$version"
+
+    local image_name="$repository:$tag"
+
+    print_info "Building image '$image_name'."
+
+    ci_container_mgr build -f "$container_file" \
+        --target "$image_type" \
+        -t "$image_name" \
+        . || die "Could not build image."
+
+    ci_container_mgr push "$image_name" || die "Could not upload image."
+}
+
+tag="${1:-1.0.0}"
+repository="${2:-ghcr.io/sdsc-ordes/tripsu}"
+container_file="$DIR/images/Containerfile"
+
+if [ "${CI:-}" = "true" ]; then
+    ci_container_mgr_login "$DOCKER_REPOSITORY_READ_USERNAME" "$DOCKER_REPOSITORY_READ_TOKEN"
+fi
+
+readarray -t images < <(grep -E "as ci-.*" "$container_file" | sed -E 's@.*as (ci-.*)$@\1@g')
+for image in "${images[@]}"; do
+    build_ci_image "$image" "$repository" "$tag"
+done
diff --git a/tools/ci/upload-image.sh b/tools/ci/upload-image.sh
new file mode 100755
index 0000000..1be4d40
--- /dev/null
+++ b/tools/ci/upload-image.sh
@@ -0,0 +1,52 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+#
+# Push image to the registry.
+
+set -euo pipefail
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+function main() {
+
+    local username=${REGISTRY_USERNAME:-$USERNAME}
+    local password=${REGISTRY_PASSWORD:-$PASSWORD}
+
+    if [ -z "$username" ] || [ -z "$password" ]; then
+        die "'USERNAME' or 'PASSWORD' env. variables not set."
+    fi
+
+    if ! ci_is_running; then
+        die "This script should only be executed in CI"
+    fi
+
+    local image_names=()
+    readarray -t image_names < <(cd build/image && find ./ -name "*.tar.gz")
+
+    for image_name in "${image_names[@]}"; do
+
+        image_path="$ROOT_DIR/build/image/$image_name"
+        image_name=${image_name%.tar.gz} # Split `.tar.gz` from end.
+        image_name=${image_name#./}      # Split `./` from front.
+        image_name=${image_name/|/:}     # Replace `|` with `:`.
+
+        print_info "Uploading image: '$image_name' in '$image_path'."
+
+        print_info "Read the image from file '$image_path' and " \
+            "directly push to registry '$image_name'."
+
+        skopeo \
+            --insecure-policy \
+            copy \
+            --dest-username "$(cat <(echo "$username"))" \
+            --dest-password "$(cat <(echo "$password"))" \
+            "docker-archive://$image_path" \
+            "docker://$image_name"
+
+    done
+}
+
+main "$@"
diff --git a/tools/format-rust.sh b/tools/format-rust.sh
new file mode 100755
index 0000000..c2a8d8f
--- /dev/null
+++ b/tools/format-rust.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+set -e
+set -u
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+fmt_args=()
+if ci_is_running; then
+    fmt_args+=("--check")
+fi
+
+cargo --version
+cargo fmt --version
+
+print_info "Run Rust format."
+cargo fmt "${fmt_args[@]}" "$@"
+
+print_info "Done."
diff --git a/tools/general.sh b/tools/general.sh
new file mode 100755
index 0000000..068bcd7
--- /dev/null
+++ b/tools/general.sh
@@ -0,0 +1,108 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+# shellcheck disable=SC2154,SC2086
+
+function _print() {
+    local color="$1"
+    local flags="$2"
+    local header="$3"
+    shift 3
+
+    local hasColor="0"
+    if [ "${FORCE_COLOR:-}" != 1 ]; then
+        [ -t 1 ] && hasColor="1"
+    else
+        hasColor="1"
+    fi
+
+    if [ "$hasColor" = "0" ] || [ "${LOG_COLORS:-}" = "false" ]; then
+        local msg
+        msg=$(printf '%b\n' "$@")
+        msg="${msg//$'\n'/$'\n'   }"
+        echo $flags -e "-- $header$msg"
+    else
+        local s=$'\033' e='[0m'
+        local msg
+        msg=$(printf "%b\n" "$@")
+        msg="${msg//$'\n'/$'\n'   }"
+        echo $flags -e "${s}${color}-- $header$msg${s}${e}"
+    fi
+}
+function print_info() {
+    _print "[0;94m" "" "" "$@"
+}
+
+function print_warning() {
+    _print "[0;31m" "" "WARN: " "$@" >&2
+}
+
+function print_error() {
+    _print "[0;31m" "" "ERROR: " "$@" >&2
+}
+
+function die() {
+    print_error "$@"
+    exit 1
+}
+
+function ci_is_running() {
+    if [ "${CI:-}" = "true" ]; then
+        return 0
+    fi
+
+    return 1
+}
+
+function ci_is_release() {
+    if [ "${CI_IS_RELEASE:-}" = "true" ]; then
+        return 0
+    fi
+
+    return 1
+}
+
+function ci_setup_git() {
+    git config --global user.name "SDSC CI"
+    git config --global user.email "ci@sdsc.ethz.ch"
+}
+
+function ci_setup_nix() {
+    local install_prefix="${1:-/usr/sbin}"
+
+    print_info "Install Nix."
+    apk add curl bash xz shadow
+    sh <(curl -L https://nixos.org/nix/install) --daemon --yes
+    cp /root/.nix-profile/bin/* "$install_prefix/"
+
+    print_info "Enable Features for Nix."
+    mkdir -p ~/.config/nix
+    {
+        echo "experimental-features = nix-command flakes"
+        echo "accept-flake-config = true"
+    } >~/.config/nix/nix.conf
+}
+
+# Run the container manager which is defined.
+# in env. variable `CONTAINER_MGR`
+# (by default `podman` if existing).
+function ci_container_mgr() {
+    local mgr="${CONTAINER_MGR:-podman}"
+
+    if command -v "$mgr" &>/dev/null; then
+        echo -e "Running '$mgr' as:\n$(printf "'%s' " "podman" "$@")" >&2
+        "$mgr" "$@"
+    else
+        echo -e "Running docker as:\n$(printf "'%s' " "docker" "$@")"
+        docker "$@"
+    fi
+}
+
+function ci_container_mgr_login() {
+    local user="$1"
+    local token="$2"
+
+    [ -n "$token" ] || die "Docker login token is empty"
+    echo "$token" |
+        ci_container_mgr login --password-stdin --username "$user" ||
+        die "Could not log into docker."
+}
diff --git a/tools/lint-rust.sh b/tools/lint-rust.sh
new file mode 100755
index 0000000..848c4d8
--- /dev/null
+++ b/tools/lint-rust.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+set -e
+set -u
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+cargo --version
+cargo clippy --version
+
+print_info "Run Rust Clippy linter."
+
+cargo clippy --no-deps -- -D warnings -A clippy::needless_return "$@" ||
+    {
+        git diff --name-status || true
+        die "Rust clippy failed."
+    }
+
+print_info "Done."
diff --git a/tools/lint-ub-rust.sh b/tools/lint-ub-rust.sh
new file mode 100755
index 0000000..71c1725
--- /dev/null
+++ b/tools/lint-ub-rust.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+set -e
+set -u
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+cd "$ROOT_DIR"
+
+cargo --version
+cargo miri --version
+
+print_info "Run Rust Miri to check undefined behaviour."
+cargo miri test "$@" ||
+    die "Rust Miri failed."
+
+print_info "Done."
diff --git a/tools/nix/flake.nix b/tools/nix/flake.nix
new file mode 100644
index 0000000..7370a33
--- /dev/null
+++ b/tools/nix/flake.nix
@@ -0,0 +1,144 @@
+{
+  description = "fuzon";
+
+  nixConfig = {
+    substituters = [
+      # Add here some other mirror if needed.
+      "https://cache.nixos.org/"
+    ];
+    extra-substituters = [
+      # Nix community's cache server
+      "https://nix-community.cachix.org"
+    ];
+    extra-trusted-public-keys = [
+      "nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs="
+    ];
+  };
+
+  inputs = {
+    # Nixpkgs
+    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
+
+    # You can access packages and modules from different nixpkgs revs
+    # at the same time. Here's an working example:
+    nixpkgsStable.url = "github:nixos/nixpkgs/nixos-23.11";
+    # Also see the 'stable-packages' overlay at 'overlays/default.nix'.
+
+    flake-utils.url = "github:numtide/flake-utils";
+
+    # The Rust overlay to include the latest toolchain.
+    rust-overlay = {
+      url = "github:oxalica/rust-overlay";
+      inputs = {
+        nixpkgs.follows = "nixpkgs";
+      };
+    };
+  };
+
+  outputs = {
+    nixpkgs,
+    flake-utils,
+    rust-overlay,
+    ...
+  }: let
+    # This is string (without toString it would be a `path` which is put into the store)
+    rootDir = toString ./. + "../../..";
+    python = pkgs.python312;
+  in
+    flake-utils.lib.eachDefaultSystem
+    # Creates an attribute map `{ devShells.<system>.default = ...}`
+    # by calling this function:
+    (
+      system: let
+        overlays = [(import rust-overlay)];
+
+        # Import nixpkgs and load it into pkgs.
+        # Overlay the rust toolchain
+        lib = nixpkgs.lib;
+        pkgs = import nixpkgs {
+          inherit system overlays;
+        };
+
+        # Set the rust toolchain from the `rust-toolchain.toml`.
+        rustToolchain = pkgs.pkgsBuildHost.rust-bin.fromRustupToolchainFile ../../rust-toolchain.toml;
+
+        # Things needed only at compile-time.
+        nativeBuildInputsBasic = with pkgs; [
+          maturin
+          findutils
+          coreutils
+          bash
+          zsh
+          curl
+          git
+          jq
+        ];
+
+        # Things needed only at compile-time.
+        nativeBuildInputsDev = with pkgs; [
+          rustToolchain
+          cargo-watch
+          just
+
+          skopeo
+          dasel
+        ];
+
+        benchInputs = with pkgs; [
+          hyperfine
+          heaptrack
+        ];
+
+        # Things needed at runtime.
+        buildInputs = [];
+
+        # The package of this CLI tool.
+        # The global version for tripsu.
+        # This is gonna get tooled later.
+        fuzon = (import ./pkgs/fuzon.nix) {
+          inherit rootDir rustToolchain pkgs lib;
+        };
+      in
+        with pkgs; rec {
+          devShells = {
+            default = mkShell {
+              inherit buildInputs;
+              nativeBuildInputs = nativeBuildInputsBasic ++ nativeBuildInputsDev;
+            };
+            bench = mkShell {
+              inherit buildInputs;
+              nativeBuildInputs = nativeBuildInputsBasic 
+                ++ nativeBuildInputsDev
+                ++ benchInputs;
+            };
+
+            ci = mkShell {
+              inherit buildInputs;
+              nativeBuildInputs = nativeBuildInputsBasic ++ nativeBuildInputsDev;
+
+              # Due to some weird handling of TMPDIR inside containers:
+              # https://github.com/NixOS/nix/issues/8355
+              # We have to reset the TMPDIR to make `nix build` work inside
+              # a development shell.
+              # Without `nix develop` it works.
+              shellHook = "unset TMPDIR";
+            };
+          };
+
+          packages = {
+            tripsu = fuzon;
+
+            images = {
+              ci = (import ./images/ci.nix) {
+                inherit pkgs;
+                devShellDrv = devShells.default;
+              };
+
+              fuzon = (import ./images/fuzon.nix) {
+                inherit pkgs fuzon;
+              };
+            };
+          };
+        }
+    );
+}
diff --git a/tools/nix/images/ci.nix b/tools/nix/images/ci.nix
new file mode 100644
index 0000000..ced142d
--- /dev/null
+++ b/tools/nix/images/ci.nix
@@ -0,0 +1,22 @@
+{
+  pkgs,
+  devShellDrv,
+  ...
+}: let
+  version = "1.0.0"; # The version of these CI images.
+  image_name = "ghcr.io/sdsc-ordes/fuzon";
+
+  buildImage = type:
+    pkgs.dockerTools.buildNixShellImage {
+      name = image_name;
+      tag = "ci-${type}-${version}";
+      drv = devShellDrv;
+    };
+in rec {
+  format = buildImage "format";
+  lint = buildImage "lint";
+  build = buildImage "build";
+  test = buildImage "test";
+  package = buildImage "package";
+  deploy = buildImage "deploy";
+}
diff --git a/tools/nix/images/fuzon.nix b/tools/nix/images/fuzon.nix
new file mode 100644
index 0000000..32ba15e
--- /dev/null
+++ b/tools/nix/images/fuzon.nix
@@ -0,0 +1,30 @@
+{
+  pkgs,
+  fuzon,
+}:
+pkgs.dockerTools.buildLayeredImage {
+  name = "ghcr.io/sdsc-ordes/fuzon";
+  tag = fuzon.version;
+
+  contents = [fuzon];
+
+  fakeRootCommands = ''
+    ${pkgs.dockerTools.shadowSetup}
+    groupadd -r non-root
+    useradd -r -g non-root non-root
+    mkdir -p /workspace
+    chown non-root:non-root /workspace
+  '';
+  enableFakechroot = true;
+
+  config = {
+    Entrypoint = ["fuzon"];
+    WorkingDir = "/workspace";
+    Labels = {
+      "org.opencontainers.image.source" = "https://github.com/sdsc-ordes/fuzon";
+      "org.opencontainers.image.description" = fuzon.meta.description;
+      "org.opencontainers.image.license" = "Apache-2.0";
+    };
+    User = "non-root";
+  };
+}
diff --git a/tools/nix/pkgs/fuzon.nix b/tools/nix/pkgs/fuzon.nix
new file mode 100644
index 0000000..29dcfd0
--- /dev/null
+++ b/tools/nix/pkgs/fuzon.nix
@@ -0,0 +1,32 @@
+{
+  pkgs,
+  lib,
+  rustToolchain,
+  rootDir,
+  ...
+}: let
+  rustPlatform = pkgs.makeRustPlatform {
+    cargo = rustToolchain;
+    rustc = rustToolchain;
+  };
+
+  cargoFile = /. + rootDir + "fuzon/Cargo.toml";
+  lockFile = /. + rootDir + "fuzon/Cargo.lock";
+in
+  rustPlatform.buildRustPackage {
+    name = "fuzon";
+    src = /. + rootDir + "fuzon/";
+
+    version = (lib.importTOML cargoFile).package.version;
+
+    cargoLock = {
+      inherit lockFile;
+    };
+
+    meta = {
+      description = "A CLI tool to fuzzy search ontology terms by their labels.";
+      homepage = "https://github.com/sdsc-ordes/fuzon";
+      license = lib.licenses.asl20;
+      maintainers = ["gabyx" "cmdoret"];
+    };
+  }
diff --git a/tools/release.sh b/tools/release.sh
new file mode 100755
index 0000000..ba3ef13
--- /dev/null
+++ b/tools/release.sh
@@ -0,0 +1,132 @@
+#!/usr/bin/env bash
+# shellcheck disable=SC1090,SC1091
+#
+# Creating a prepare tag to trigger the release process on the
+# Github workflow. Can only be called on `main`.
+#
+# Usage: release.sh "1.2.0"
+
+set -euo pipefail
+
+ROOT_DIR=$(git rev-parse --show-toplevel)
+. "$ROOT_DIR/tools/general.sh"
+
+RELEASE_BRANCH="${RELEASE_BRANCH:-main}"
+VERSION_FILE="$ROOT_DIR/Cargo.toml"
+
+function delete_prepare_tags() {
+    readarray -t prepareTag < <(git tag --list "prepare-*")
+
+    for tag in "${prepareTag[@]}"; do
+        print_info "Deleting prepare tag '$tag'."
+        git push -f origin ":${tag}" || true
+        git tag -d "$tag" || die
+    done
+}
+
+function create_prepare_tag() {
+    local tag="$1"
+
+    print_info "Tagging with '$tag'."
+    git tag -a -m "Version $version" "$tag" || die "Could not create tag."
+
+    print_info "Tag contains:"
+    git cat-file -p "$tag" || die "Could not show tag content."
+
+    print_info "Successfully created prepate tag '$tag'."
+}
+
+function commit_version_file() {
+    local version="$1"
+    print_info "Writing new version file... (for Nix)"
+
+    dasel put -r toml -f "$VERSION_FILE" -t string -v "$version" .package.version
+
+    if ! git diff --exit-code --quiet; then
+        # Commit if we have change.
+        git add "$VERSION_FILE"
+        git commit -m "chore: release '$version'"
+    fi
+}
+
+function trigger_build() {
+    local branch="$1"
+    local tag="$2"
+
+    printf "Do you want to trigger the build? [y|n]: "
+    read -r answer
+    if [ "$answer" != "y" ]; then
+        die "Do not trigger build -> abort."
+    fi
+
+    print_info "Pushing tag '$tag'."
+    git push -f origin --no-follow-tags "$branch" "$tag"
+
+    print_info "Successfully triggered build."
+}
+
+function check_new_version() {
+    local new_version="$1"
+
+    # Check that is a version.
+    if [ "$(ci_container_mgr run --rm docker.io/alpine/semver semver "$new_version" | tail -1)" != "$new_version" ]; then
+        die "Your version '$new_version' is not sem. version compliant."
+    fi
+
+    if git tag --list "v*" | grep -qE "^v$new_version$"; then
+        die "Git tag 'v$new_version' already exists locally."
+    fi
+
+    # Get all remote versions.
+    local remote_versions=()
+    readarray -t remote_versions < \
+        <(git ls-remote origin "regs/tags/v*" | cut -f 2 | sed "s@/refs/tags/v@@g")
+
+    # shellcheck disable=SC2128
+    if [ "${#remote_versions[@]}" = "0" ]; then
+        # No version tags yet. Its ok.
+        return 0
+    fi
+
+    if echo "${remote_versions[@]}" | grep "$new_version"; then
+        die "Remote already contains version tag 'v$new_version'".
+    fi
+
+    # Sort the versions.
+    # The top version must be the new one!
+    latest=$(ci_container_mgr run --rm alpine/semver semver "${remote_versions[@]}" "$new_version" | tail -1)
+
+    if [ "$latest" != "$new_version" ]; then
+        die "Your version '$new_version' is not newer than the remote ones:" \
+            "${remote_versions[@]}"
+    fi
+}
+
+function main() {
+    cd "$ROOT_DIR"
+
+    local version="$1"
+
+    local branch
+    branch=$(git branch --show-current)
+
+    if [ "$branch" != "$RELEASE_BRANCH" ] && [ "${FORCE_RELEASE:-}" != "true" ]; then
+        die "Can only tag on 'main'. Use 'FORCE_RELEASE=true'."
+    fi
+
+    if ! git diff --quiet --exit-code; then
+        die "You have changes on this branch."
+    fi
+
+    delete_prepare_tags
+
+    local prepare_tag="prepare-v$version"
+
+    check_new_version "$version"
+    commit_version_file "$version"
+
+    create_prepare_tag "$prepare_tag"
+    trigger_build "$branch" "$prepare_tag"
+}
+
+main "$@"

From 31e4bf8f490dec4e45cb9a53665226b49de30875 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 16:55:52 +0200
Subject: [PATCH 07/18] chore: migrate tooling tripsu->fuzon

---
 tools/bench/benchmark.sh          | 91 +++++++---------------------
 tools/build-image.sh              |  6 +-
 tools/build-package.sh            |  2 +-
 tools/ci/create-github-release.sh |  2 +-
 tools/ci/images/Containerfile     |  4 +-
 tools/ci/upload-ci-images.sh      |  2 +-
 tools/nix/flake.lock              | 99 +++++++++++++++++++++++++++++++
 tools/nix/flake.nix               |  6 +-
 8 files changed, 131 insertions(+), 81 deletions(-)
 create mode 100644 tools/nix/flake.lock

diff --git a/tools/bench/benchmark.sh b/tools/bench/benchmark.sh
index 30db925..d98eb59 100644
--- a/tools/bench/benchmark.sh
+++ b/tools/bench/benchmark.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# Benchmark runtime and memory usage of tripsu
+# Benchmark runtime and memory usage of fuzon
 # Compares the working directory version against a baseline branch (main by default)
 
 set -euo pipefail
@@ -26,52 +26,29 @@ BASE_URL="$(git config --get remote.origin.url)"
     && cd "${BASE_DIR}" \
     && just build "${BUILD_ARGS[@]}"
 )
-BASE_BIN="${BASE_DIR}/target/${PROFILE}/tripsu"
+BASE_BIN="${BASE_DIR}/target/${PROFILE}/fuzon"
 
 # current binary
 COMP_BRANCH="$(git rev-parse --abbrev-ref HEAD)"
 just build "${BUILD_ARGS[@]}"
-COMP_BIN="./target/${PROFILE}/tripsu"
+COMP_BIN="./target/${PROFILE}/fuzon"
 
 # setup data
 DATA_URL="https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/proteomes.rdf.xz"
-INPUT="/tmp/proteomes.nt"
+INPUT="/tmp/proteomes.ttl"
 
 # Download data if needed
 if [ ! -f ${INPUT} ]; then
     curl "${DATA_URL}" \
     | xz -dc -  \
-    | rdfpipe-rs -i rdf-xml -o nt - \
+    | rdfpipe-rs -i rdf-xml -o ttl - \
     > "${INPUT}" || rm "${INPUT}"
 fi
 
-# setup config
-RULES=$(mktemp)
-BASE_IDX=$(mktemp)
-COMP_IDX=$(mktemp)
-
-cat << EOF > "${RULES}"
-
-nodes:
-  of_type:
-    - "http://purl.uniprot.org/core/Proteome"
-    - "http://purl.uniprot.org/core/Strain"
-
-objects:
-  on_type_predicate:
-    "http://purl.uniprot.org/core/Submission_Citation":
-      - "http://purl.uniprot.org/core/author"
-  
-  on_predicate:
-    - "http://purl.org/dc/terms/identifier"
-
-EOF
-
 ### Commands to benchmark
-BASE_CMD_IDX="${BASE_BIN} index -o ${BASE_IDX} ${INPUT}"
-COMP_CMD_IDX="${COMP_BIN} index -o ${COMP_IDX} ${INPUT}"
-BASE_CMD_PSD="${BASE_BIN} pseudo -r ${RULES} -x ${BASE_IDX} ${INPUT}"
-COMP_CMD_PSD="${COMP_BIN} pseudo -r ${RULES} -x ${COMP_IDX} ${INPUT}"
+QUERY="tein"
+BASE_CMD="${BASE_BIN} index -t100 -q ${QUERY} -s ${INPUT}"
+COMP_CMD="${COMP_BIN} index -t100 -q ${QUERY} -s ${INPUT}"
 
 ### functions for profiling
 
@@ -99,14 +76,12 @@ mem_prof() {
 }
 
 make_report() {
-    local cpu_index=$1
-    local cpu_pseudo=$2
-    local mem_index=$3
-    local mem_pseudo=$4
-    local base_branch=$5
+    local cpu=$1
+    local mem=$2
+    local base_branch=$3
 
     cat <<-MD
-	# tripsu profiling
+	# fuzon profiling
 
 	> date: $(date -u +%Y-%m-%d)
 
@@ -116,25 +91,14 @@ make_report() {
 	
 	Run time compared using hyperfine
 	
-	### Indexing
-	
-	$(cat "${cpu_index}")
-	
-	### Pseudonymization
-	
-	$(cat "${cpu_pseudo}")
+	$(cat "${cpu}")
 	
 	## Memory
 	
 	Heap memory usage compared using heaptrack
 	
-	### Indexing
-	
-	$(cat "${mem_index}")
-	
-	### Pseudonymization
+	$(cat "${mem}")
 	
-	$(cat "${mem_pseudo}")
 	MD
 }
 
@@ -142,30 +106,17 @@ make_report() {
 ###  Run profiling
 
 ## Profile cpu time
-HYPF_IDX_OUT=$(mktemp)
-HYPF_PSD_OUT=$(mktemp)
+HYPF_OUT=$(mktemp)
 
-# indexing
-cpu_prof "${BASE_BRANCH}" "${BASE_CMD_IDX}" \
-         "${COMP_BRANCH}" "${COMP_CMD_IDX}" "${HYPF_IDX_OUT}"
-# pseudonymization
-cpu_prof "${BASE_BRANCH}" "${BASE_CMD_IDX}" \
-         "${COMP_BRANCH}" "${COMP_CMD_IDX}" "${HYPF_PSD_OUT}"
+cpu_prof "${BASE_BRANCH}" "${BASE_CMD}" \
+         "${COMP_BRANCH}" "${COMP_CMD}" "${HYPF_OUT}"
 
 ## Profile memory
-HEAP_IDX_OUT=$(mktemp)
-HEAP_PSD_OUT=$(mktemp)
+HEAP_OUT=$(mktemp)
 
-# indexing
-mem_prof "${BASE_BRANCH}" "${BASE_CMD_IDX}" >  "${HEAP_IDX_OUT}"
-mem_prof "${COMP_BRANCH}" "${COMP_CMD_IDX}" >> "${HEAP_IDX_OUT}"
-# pseudonymization
-mem_prof "${BASE_BRANCH}" "${BASE_CMD_PSD}" >  "${HEAP_PSD_OUT}"
-mem_prof "${COMP_BRANCH}" "${COMP_CMD_PSD}" >> "${HEAP_PSD_OUT}"
+mem_prof "${BASE_BRANCH}" "${BASE_CMD}" >  "${HEAP_OUT}"
+mem_prof "${COMP_BRANCH}" "${COMP_CMD}" >> "${HEAP_OUT}"
 
 
 ### Reporting
-make_report \
-    "${HYPF_IDX_OUT}" "${HYPF_PSD_OUT}" \
-    "${HEAP_IDX_OUT}" "${HEAP_PSD_OUT}" \
-    "${BASE_BRANCH}" > "${OUTPUT}"
+make_report "${HYPF_OUT}" "${HEAP_OUT}" "${BASE_BRANCH}" > "${OUTPUT}"
diff --git a/tools/build-image.sh b/tools/build-image.sh
index 11459c7..2084faa 100755
--- a/tools/build-image.sh
+++ b/tools/build-image.sh
@@ -49,8 +49,8 @@ function main() {
         fi
     fi
 
-    image_name=$(nix eval --raw "./tools/nix#images.tripsu.imageName")
-    image_tag=$(nix eval --raw "./tools/nix#images.tripsu.imageTag")
+    image_name=$(nix eval --raw "./tools/nix#images.fuzon.imageName")
+    image_tag=$(nix eval --raw "./tools/nix#images.fuzon.imageTag")
 
     # We cannot use `:` before the tag, because `skopeo`
     # is unable to read this path correctly, because it
@@ -61,7 +61,7 @@ function main() {
 
     print_info "Building image '$dir'."
     nix --version
-    nix build -L "./tools/nix#images.tripsu" \
+    nix build -L "./tools/nix#images.fuzon" \
         --out-link "$dir" "${args[@]}"
 }
 
diff --git a/tools/build-package.sh b/tools/build-package.sh
index 3d9d1c1..45be2df 100755
--- a/tools/build-package.sh
+++ b/tools/build-package.sh
@@ -14,6 +14,6 @@ dir="build/package"
 
 print_info "Building the package."
 nix --version
-nix build -L "./tools/nix#tripsu" \
+nix build -L "./tools/nix#fuzon" \
     --out-link "$dir" \
     "$@"
diff --git a/tools/ci/create-github-release.sh b/tools/ci/create-github-release.sh
index 2c0102c..f6b9b77 100755
--- a/tools/ci/create-github-release.sh
+++ b/tools/ci/create-github-release.sh
@@ -18,7 +18,7 @@ function main() {
 
     gh release create "$tag" \
         --repo="$repo" \
-        --title="tripsu: $version" \
+        --title="fuzon: $version" \
         --generate-notes
 
     print_info "Successfully created release. All done."
diff --git a/tools/ci/images/Containerfile b/tools/ci/images/Containerfile
index 27c23cf..2b1f2eb 100644
--- a/tools/ci/images/Containerfile
+++ b/tools/ci/images/Containerfile
@@ -4,8 +4,8 @@
 # do other non-docker related stuff.
 
 FROM alpine:latest as base-podman
-LABEL org.opencontainers.image.source https://github.com/sdsc-ordes/tripsu
-LABEL org.opencontainers.image.description "CI container image for tripsu"
+LABEL org.opencontainers.image.source https://github.com/sdsc-ordes/fuzon
+LABEL org.opencontainers.image.description "CI container image for fuzon"
 LABEL org.opencontainers.image.license "Apache"
 
 RUN apk add findutils coreutils git jq curl bash just parallel podman
diff --git a/tools/ci/upload-ci-images.sh b/tools/ci/upload-ci-images.sh
index d67d092..3afcf72 100755
--- a/tools/ci/upload-ci-images.sh
+++ b/tools/ci/upload-ci-images.sh
@@ -28,7 +28,7 @@ function build_ci_image() {
 }
 
 tag="${1:-1.0.0}"
-repository="${2:-ghcr.io/sdsc-ordes/tripsu}"
+repository="${2:-ghcr.io/sdsc-ordes/fuzon}"
 container_file="$DIR/images/Containerfile"
 
 if [ "${CI:-}" = "true" ]; then
diff --git a/tools/nix/flake.lock b/tools/nix/flake.lock
new file mode 100644
index 0000000..51cc2df
--- /dev/null
+++ b/tools/nix/flake.lock
@@ -0,0 +1,99 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1710146030,
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1725432240,
+        "narHash": "sha256-+yj+xgsfZaErbfYM3T+QvEE2hU7UuE+Jf0fJCJ8uPS0=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "ad416d066ca1222956472ab7d0555a6946746a80",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgsStable": {
+      "locked": {
+        "lastModified": 1720535198,
+        "narHash": "sha256-zwVvxrdIzralnSbcpghA92tWu2DV2lwv89xZc8MTrbg=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "205fd4226592cc83fd4c0885a3e4c9c400efabb5",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "nixos-23.11",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "nixpkgsStable": "nixpkgsStable",
+        "rust-overlay": "rust-overlay"
+      }
+    },
+    "rust-overlay": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1725589472,
+        "narHash": "sha256-+OB00N6Yql/ZRQQkQ0PNnxfW2tH89DHnv29hBS7tXMM=",
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "rev": "2b00881d2ff72174cffdc007238cb6bedd6e1d8e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "oxalica",
+        "repo": "rust-overlay",
+        "type": "github"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/tools/nix/flake.nix b/tools/nix/flake.nix
index 7370a33..24002d7 100644
--- a/tools/nix/flake.nix
+++ b/tools/nix/flake.nix
@@ -43,7 +43,7 @@
   }: let
     # This is string (without toString it would be a `path` which is put into the store)
     rootDir = toString ./. + "../../..";
-    python = pkgs.python312;
+    python = nixpkgs.python312;
   in
     flake-utils.lib.eachDefaultSystem
     # Creates an attribute map `{ devShells.<system>.default = ...}`
@@ -93,7 +93,7 @@
         buildInputs = [];
 
         # The package of this CLI tool.
-        # The global version for tripsu.
+        # The global version for fuzon.
         # This is gonna get tooled later.
         fuzon = (import ./pkgs/fuzon.nix) {
           inherit rootDir rustToolchain pkgs lib;
@@ -126,7 +126,7 @@
           };
 
           packages = {
-            tripsu = fuzon;
+            fuzon = fuzon;
 
             images = {
               ci = (import ./images/ci.nix) {

From 07a43e2b2c475b6d51718f7330bb8e266e4c7359 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 17:12:27 +0200
Subject: [PATCH 08/18] chore: target crate path in nix flake

---
 tools/nix/pkgs/fuzon.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/nix/pkgs/fuzon.nix b/tools/nix/pkgs/fuzon.nix
index 29dcfd0..e31dab2 100644
--- a/tools/nix/pkgs/fuzon.nix
+++ b/tools/nix/pkgs/fuzon.nix
@@ -10,12 +10,12 @@
     rustc = rustToolchain;
   };
 
-  cargoFile = /. + rootDir + "fuzon/Cargo.toml";
-  lockFile = /. + rootDir + "fuzon/Cargo.lock";
+  cargoFile = /. + rootDir + "/fuzon/Cargo.toml";
+  lockFile = /. + rootDir + "/fuzon/Cargo.lock";
 in
   rustPlatform.buildRustPackage {
     name = "fuzon";
-    src = /. + rootDir + "fuzon/";
+    src = /. + rootDir;
 
     version = (lib.importTOML cargoFile).package.version;
 

From a64856f4c7fa6bb3b2e89fea1a0d36008c4533e1 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 17:18:57 +0200
Subject: [PATCH 09/18] chore: add just recipe for nix dev

---
 justfile | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/justfile b/justfile
index 606e23e..0e2c53d 100644
--- a/justfile
+++ b/justfile
@@ -13,9 +13,15 @@ build *args:
     --release \
     {{args}}
 
-# development environment
-py-develop *args:
+# install editable python package
+maturin-dev *args:
   maturin develop \
   --manifest-path pyfuzon/Cargo.toml \
   --uv \
   {{args}}
+
+nix-develop *args:
+  cd {{root}} && \
+  cmd=("$@") && \
+  { [ -n "${cmd:-}" ] || cmd=("zsh"); } && \
+  nix develop ./tools/nix#default --command "${cmd[@]}"

From b0136eae1fbc5ca1b7d4dc4524e6a70812fd9e97 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 17:25:04 +0200
Subject: [PATCH 10/18] docs(readme): describe python api

---
 README.md | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 8616b31..9f3dac8 100644
--- a/README.md
+++ b/README.md
@@ -28,10 +28,9 @@ To filter the top 3 matches in a file non-interactively:
 $ fuzon -q 'aspirin' --top 3 -s onto1.ttl -s onto2.ttl
 ```
 
+Running fuzon without a query will start an interactive prompt to browse the input ontologies.
 
-Not implemented yet: ~~Running fuzon with a set of RDF ontologies / terminologies will start an interactive prompt using [fzf](https://github.com/junegunn/fzf) to browse the input ontologies.~~
-
-### rust crate
+### rust library
 ```rust
 use fuzon;
 let r1 = BufReader::new(File::open("onto1.ttl")) 
@@ -44,3 +43,12 @@ matcher.rank_terms("some query")
 
 ### python package
 
+```python
+from pyfuzon.matcher import TermMatcher
+
+matcher = TermMatcher.from_files("https://example.org/onto1.ttl", "/data/onto2.ttl")
+matcher.terms #accesses the list of terms loaded from input files
+matcher.score("query") # returns the match score of each term for the input query.
+matcher.rank("query") # returns the list of terms sorted by similarity with the query.
+matcher.top("query", 5) # shows top 5 most similar results (sorted).
+```

From 1e3f74950cc9ee6d1ed563e853662f5b4bcd7f98 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 17:27:56 +0200
Subject: [PATCH 11/18] docs(readme): minimal development instructions

---
 README.md | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 9f3dac8..14f1705 100644
--- a/README.md
+++ b/README.md
@@ -18,9 +18,7 @@ cargo build --release
 
 ## usage
 
-### Command line interface
-
-
+### command line interface
 
 To filter the top 3 matches in a file non-interactively:
 
@@ -40,7 +38,6 @@ let matcher = TermMatcher::from_readers(vec![r1, r2])
 matcher.rank_terms("some query")
 ```
 
-
 ### python package
 
 ```python
@@ -52,3 +49,12 @@ matcher.score("query") # returns the match score of each term for the input quer
 matcher.rank("query") # returns the list of terms sorted by similarity with the query.
 matcher.top("query", 5) # shows top 5 most similar results (sorted).
 ```
+
+## development
+
+A nix dev shell with all build dependencies is provided.
+Assuming just and nix are installed on the machine, you can enter the shell with:
+
+```shell
+just nix-develop
+```

From c38185d441f6132f86089de683401161b1ef7421 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 17:35:32 +0200
Subject: [PATCH 12/18] chore: rm unneeded tooling

---
 tools/build-image.sh   |  68 ---------------------
 tools/build-package.sh |  19 ------
 tools/format-rust.sh   |  22 -------
 tools/general.sh       | 108 ---------------------------------
 tools/lint-rust.sh     |  22 -------
 tools/lint-ub-rust.sh  |  18 ------
 tools/release.sh       | 132 -----------------------------------------
 7 files changed, 389 deletions(-)
 delete mode 100755 tools/build-image.sh
 delete mode 100755 tools/build-package.sh
 delete mode 100755 tools/format-rust.sh
 delete mode 100755 tools/general.sh
 delete mode 100755 tools/lint-rust.sh
 delete mode 100755 tools/lint-ub-rust.sh
 delete mode 100755 tools/release.sh

diff --git a/tools/build-image.sh b/tools/build-image.sh
deleted file mode 100755
index 2084faa..0000000
--- a/tools/build-image.sh
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-#
-# Build the Nix container image.
-
-set -euo pipefail
-
-ROOT_DIR=$(git rev-parse --show-toplevel)
-. "$ROOT_DIR/tools/general.sh"
-
-VERSION_FILE="$ROOT_DIR/Cargo.toml"
-
-function clean_up() {
-    if ! ci_is_running; then
-        # Never change the version file, only
-        # on explicit `just release`.
-        print_info "Restoring '$VERSION_FILE'."
-        git restore "$VERSION_FILE" || true
-    fi
-}
-
-trap clean_up EXIT
-
-function main() {
-    args=("$@")
-
-    if ! ci_is_running || ! ci_is_release; then
-        print_info "Building image for development."
-
-        # Define the image version from Git SHA
-        version="0.0.0-dev.$(git rev-parse --short=7 HEAD)"
-
-        # Write the temporary version file (gets restored...)
-        dasel put -r toml -f "$VERSION_FILE" -t string -v "$version" .package.version
-    else
-        print_info "Building image for release."
-
-        # When CI and in Release, the requested version must match.
-        version=$(dasel -r toml -f "$VERSION_FILE" .package.version -w yaml)
-
-        release_version=${GITHUB_REF##*prepare-v}
-
-        if [ "$version" != "$release_version" ]; then
-            die "The version '$version' in '$VERSION_FILE' does not corresponds" \
-                "with the version '$release_version' to build." \
-                "Update the version file to align!" \
-                "Nix is pure and cannot rely on Git tags to" \
-                "get the version from."
-        fi
-    fi
-
-    image_name=$(nix eval --raw "./tools/nix#images.fuzon.imageName")
-    image_tag=$(nix eval --raw "./tools/nix#images.fuzon.imageTag")
-
-    # We cannot use `:` before the tag, because `skopeo`
-    # is unable to read this path correctly, because it
-    # stupidly deals with it.
-    dir="build/image/$image_name|$image_tag.tar.gz"
-
-    cd "$ROOT_DIR"
-
-    print_info "Building image '$dir'."
-    nix --version
-    nix build -L "./tools/nix#images.fuzon" \
-        --out-link "$dir" "${args[@]}"
-}
-
-main "$@"
diff --git a/tools/build-package.sh b/tools/build-package.sh
deleted file mode 100755
index 45be2df..0000000
--- a/tools/build-package.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-#
-# Build the Nix container image.
-
-set -euo pipefail
-
-ROOT_DIR=$(git rev-parse --show-toplevel)
-. "$ROOT_DIR/tools/general.sh"
-
-cd "$ROOT_DIR"
-
-dir="build/package"
-
-print_info "Building the package."
-nix --version
-nix build -L "./tools/nix#fuzon" \
-    --out-link "$dir" \
-    "$@"
diff --git a/tools/format-rust.sh b/tools/format-rust.sh
deleted file mode 100755
index c2a8d8f..0000000
--- a/tools/format-rust.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-set -e
-set -u
-
-ROOT_DIR=$(git rev-parse --show-toplevel)
-. "$ROOT_DIR/tools/general.sh"
-
-cd "$ROOT_DIR"
-
-fmt_args=()
-if ci_is_running; then
-    fmt_args+=("--check")
-fi
-
-cargo --version
-cargo fmt --version
-
-print_info "Run Rust format."
-cargo fmt "${fmt_args[@]}" "$@"
-
-print_info "Done."
diff --git a/tools/general.sh b/tools/general.sh
deleted file mode 100755
index 068bcd7..0000000
--- a/tools/general.sh
+++ /dev/null
@@ -1,108 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-# shellcheck disable=SC2154,SC2086
-
-function _print() {
-    local color="$1"
-    local flags="$2"
-    local header="$3"
-    shift 3
-
-    local hasColor="0"
-    if [ "${FORCE_COLOR:-}" != 1 ]; then
-        [ -t 1 ] && hasColor="1"
-    else
-        hasColor="1"
-    fi
-
-    if [ "$hasColor" = "0" ] || [ "${LOG_COLORS:-}" = "false" ]; then
-        local msg
-        msg=$(printf '%b\n' "$@")
-        msg="${msg//$'\n'/$'\n'   }"
-        echo $flags -e "-- $header$msg"
-    else
-        local s=$'\033' e='[0m'
-        local msg
-        msg=$(printf "%b\n" "$@")
-        msg="${msg//$'\n'/$'\n'   }"
-        echo $flags -e "${s}${color}-- $header$msg${s}${e}"
-    fi
-}
-function print_info() {
-    _print "[0;94m" "" "" "$@"
-}
-
-function print_warning() {
-    _print "[0;31m" "" "WARN: " "$@" >&2
-}
-
-function print_error() {
-    _print "[0;31m" "" "ERROR: " "$@" >&2
-}
-
-function die() {
-    print_error "$@"
-    exit 1
-}
-
-function ci_is_running() {
-    if [ "${CI:-}" = "true" ]; then
-        return 0
-    fi
-
-    return 1
-}
-
-function ci_is_release() {
-    if [ "${CI_IS_RELEASE:-}" = "true" ]; then
-        return 0
-    fi
-
-    return 1
-}
-
-function ci_setup_git() {
-    git config --global user.name "SDSC CI"
-    git config --global user.email "ci@sdsc.ethz.ch"
-}
-
-function ci_setup_nix() {
-    local install_prefix="${1:-/usr/sbin}"
-
-    print_info "Install Nix."
-    apk add curl bash xz shadow
-    sh <(curl -L https://nixos.org/nix/install) --daemon --yes
-    cp /root/.nix-profile/bin/* "$install_prefix/"
-
-    print_info "Enable Features for Nix."
-    mkdir -p ~/.config/nix
-    {
-        echo "experimental-features = nix-command flakes"
-        echo "accept-flake-config = true"
-    } >~/.config/nix/nix.conf
-}
-
-# Run the container manager which is defined.
-# in env. variable `CONTAINER_MGR`
-# (by default `podman` if existing).
-function ci_container_mgr() {
-    local mgr="${CONTAINER_MGR:-podman}"
-
-    if command -v "$mgr" &>/dev/null; then
-        echo -e "Running '$mgr' as:\n$(printf "'%s' " "podman" "$@")" >&2
-        "$mgr" "$@"
-    else
-        echo -e "Running docker as:\n$(printf "'%s' " "docker" "$@")"
-        docker "$@"
-    fi
-}
-
-function ci_container_mgr_login() {
-    local user="$1"
-    local token="$2"
-
-    [ -n "$token" ] || die "Docker login token is empty"
-    echo "$token" |
-        ci_container_mgr login --password-stdin --username "$user" ||
-        die "Could not log into docker."
-}
diff --git a/tools/lint-rust.sh b/tools/lint-rust.sh
deleted file mode 100755
index 848c4d8..0000000
--- a/tools/lint-rust.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-set -e
-set -u
-
-ROOT_DIR=$(git rev-parse --show-toplevel)
-. "$ROOT_DIR/tools/general.sh"
-
-cd "$ROOT_DIR"
-
-cargo --version
-cargo clippy --version
-
-print_info "Run Rust Clippy linter."
-
-cargo clippy --no-deps -- -D warnings -A clippy::needless_return "$@" ||
-    {
-        git diff --name-status || true
-        die "Rust clippy failed."
-    }
-
-print_info "Done."
diff --git a/tools/lint-ub-rust.sh b/tools/lint-ub-rust.sh
deleted file mode 100755
index 71c1725..0000000
--- a/tools/lint-ub-rust.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-set -e
-set -u
-
-ROOT_DIR=$(git rev-parse --show-toplevel)
-. "$ROOT_DIR/tools/general.sh"
-
-cd "$ROOT_DIR"
-
-cargo --version
-cargo miri --version
-
-print_info "Run Rust Miri to check undefined behaviour."
-cargo miri test "$@" ||
-    die "Rust Miri failed."
-
-print_info "Done."
diff --git a/tools/release.sh b/tools/release.sh
deleted file mode 100755
index ba3ef13..0000000
--- a/tools/release.sh
+++ /dev/null
@@ -1,132 +0,0 @@
-#!/usr/bin/env bash
-# shellcheck disable=SC1090,SC1091
-#
-# Creating a prepare tag to trigger the release process on the
-# Github workflow. Can only be called on `main`.
-#
-# Usage: release.sh "1.2.0"
-
-set -euo pipefail
-
-ROOT_DIR=$(git rev-parse --show-toplevel)
-. "$ROOT_DIR/tools/general.sh"
-
-RELEASE_BRANCH="${RELEASE_BRANCH:-main}"
-VERSION_FILE="$ROOT_DIR/Cargo.toml"
-
-function delete_prepare_tags() {
-    readarray -t prepareTag < <(git tag --list "prepare-*")
-
-    for tag in "${prepareTag[@]}"; do
-        print_info "Deleting prepare tag '$tag'."
-        git push -f origin ":${tag}" || true
-        git tag -d "$tag" || die
-    done
-}
-
-function create_prepare_tag() {
-    local tag="$1"
-
-    print_info "Tagging with '$tag'."
-    git tag -a -m "Version $version" "$tag" || die "Could not create tag."
-
-    print_info "Tag contains:"
-    git cat-file -p "$tag" || die "Could not show tag content."
-
-    print_info "Successfully created prepate tag '$tag'."
-}
-
-function commit_version_file() {
-    local version="$1"
-    print_info "Writing new version file... (for Nix)"
-
-    dasel put -r toml -f "$VERSION_FILE" -t string -v "$version" .package.version
-
-    if ! git diff --exit-code --quiet; then
-        # Commit if we have change.
-        git add "$VERSION_FILE"
-        git commit -m "chore: release '$version'"
-    fi
-}
-
-function trigger_build() {
-    local branch="$1"
-    local tag="$2"
-
-    printf "Do you want to trigger the build? [y|n]: "
-    read -r answer
-    if [ "$answer" != "y" ]; then
-        die "Do not trigger build -> abort."
-    fi
-
-    print_info "Pushing tag '$tag'."
-    git push -f origin --no-follow-tags "$branch" "$tag"
-
-    print_info "Successfully triggered build."
-}
-
-function check_new_version() {
-    local new_version="$1"
-
-    # Check that is a version.
-    if [ "$(ci_container_mgr run --rm docker.io/alpine/semver semver "$new_version" | tail -1)" != "$new_version" ]; then
-        die "Your version '$new_version' is not sem. version compliant."
-    fi
-
-    if git tag --list "v*" | grep -qE "^v$new_version$"; then
-        die "Git tag 'v$new_version' already exists locally."
-    fi
-
-    # Get all remote versions.
-    local remote_versions=()
-    readarray -t remote_versions < \
-        <(git ls-remote origin "regs/tags/v*" | cut -f 2 | sed "s@/refs/tags/v@@g")
-
-    # shellcheck disable=SC2128
-    if [ "${#remote_versions[@]}" = "0" ]; then
-        # No version tags yet. Its ok.
-        return 0
-    fi
-
-    if echo "${remote_versions[@]}" | grep "$new_version"; then
-        die "Remote already contains version tag 'v$new_version'".
-    fi
-
-    # Sort the versions.
-    # The top version must be the new one!
-    latest=$(ci_container_mgr run --rm alpine/semver semver "${remote_versions[@]}" "$new_version" | tail -1)
-
-    if [ "$latest" != "$new_version" ]; then
-        die "Your version '$new_version' is not newer than the remote ones:" \
-            "${remote_versions[@]}"
-    fi
-}
-
-function main() {
-    cd "$ROOT_DIR"
-
-    local version="$1"
-
-    local branch
-    branch=$(git branch --show-current)
-
-    if [ "$branch" != "$RELEASE_BRANCH" ] && [ "${FORCE_RELEASE:-}" != "true" ]; then
-        die "Can only tag on 'main'. Use 'FORCE_RELEASE=true'."
-    fi
-
-    if ! git diff --quiet --exit-code; then
-        die "You have changes on this branch."
-    fi
-
-    delete_prepare_tags
-
-    local prepare_tag="prepare-v$version"
-
-    check_new_version "$version"
-    commit_version_file "$version"
-
-    create_prepare_tag "$prepare_tag"
-    trigger_build "$branch" "$prepare_tag"
-}
-
-main "$@"

From e05c8aadeba25dc876ae30a7a6e79d1a1890de15 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 18:31:30 +0200
Subject: [PATCH 13/18] refactor(nix): simplify dev image setup

---
 justfile                 | 29 ++++++++++++++++++++++++-----
 tools/nix/flake.nix      | 13 +------------
 tools/nix/images/ci.nix  | 22 ----------------------
 tools/nix/images/dev.nix | 10 ++++++++++
 4 files changed, 35 insertions(+), 39 deletions(-)
 delete mode 100644 tools/nix/images/ci.nix
 create mode 100644 tools/nix/images/dev.nix

diff --git a/justfile b/justfile
index 0e2c53d..b54bda6 100644
--- a/justfile
+++ b/justfile
@@ -20,8 +20,27 @@ maturin-dev *args:
   --uv \
   {{args}}
 
-nix-develop *args:
-  cd {{root}} && \
-  cmd=("$@") && \
-  { [ -n "${cmd:-}" ] || cmd=("zsh"); } && \
-  nix develop ./tools/nix#default --command "${cmd[@]}"
+develop-nix *args:
+  cd {{root}} \
+    && cmd=("$@") \
+    && { [ -n "${cmd:-}" ] || cmd=("zsh"); } \
+    && nix develop ./tools/nix#default --command "${cmd[@]}"
+
+develop-docker:
+  docker run \
+    --user 1000:1000 \
+    -it \
+    -w "/build/workspace" \
+    --mount type=bind,source="$(pwd)",target=/build/work \
+    {{image}}:dev
+
+# maintenance
+
+image-build:
+  nix build -L "./tools/nix#image.dev" --out-link "target/image.dev" \
+    && docker load < "build/image.dev"
+  nix build -L "./tools/nix#image.fuzon" --out-link "target/image.fuzon" \
+    && docker load < "build/image.fuzon"
+
+
+
diff --git a/tools/nix/flake.nix b/tools/nix/flake.nix
index 24002d7..64bafc7 100644
--- a/tools/nix/flake.nix
+++ b/tools/nix/flake.nix
@@ -112,24 +112,13 @@
                 ++ benchInputs;
             };
 
-            ci = mkShell {
-              inherit buildInputs;
-              nativeBuildInputs = nativeBuildInputsBasic ++ nativeBuildInputsDev;
-
-              # Due to some weird handling of TMPDIR inside containers:
-              # https://github.com/NixOS/nix/issues/8355
-              # We have to reset the TMPDIR to make `nix build` work inside
-              # a development shell.
-              # Without `nix develop` it works.
-              shellHook = "unset TMPDIR";
-            };
           };
 
           packages = {
             fuzon = fuzon;
 
             images = {
-              ci = (import ./images/ci.nix) {
+              dev = (import ./images/dev.nix) {
                 inherit pkgs;
                 devShellDrv = devShells.default;
               };
diff --git a/tools/nix/images/ci.nix b/tools/nix/images/ci.nix
deleted file mode 100644
index ced142d..0000000
--- a/tools/nix/images/ci.nix
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-  pkgs,
-  devShellDrv,
-  ...
-}: let
-  version = "1.0.0"; # The version of these CI images.
-  image_name = "ghcr.io/sdsc-ordes/fuzon";
-
-  buildImage = type:
-    pkgs.dockerTools.buildNixShellImage {
-      name = image_name;
-      tag = "ci-${type}-${version}";
-      drv = devShellDrv;
-    };
-in rec {
-  format = buildImage "format";
-  lint = buildImage "lint";
-  build = buildImage "build";
-  test = buildImage "test";
-  package = buildImage "package";
-  deploy = buildImage "deploy";
-}
diff --git a/tools/nix/images/dev.nix b/tools/nix/images/dev.nix
new file mode 100644
index 0000000..5734d92
--- /dev/null
+++ b/tools/nix/images/dev.nix
@@ -0,0 +1,10 @@
+{ pkgs, devShellDrv, ... }:
+
+let
+  image_name = "ghcr.io/sdsc-ordes/fuzon";
+
+in pkgs.dockerTools.buildNixShellImage {
+      name = image_name;
+      tag = "dev";
+      drv = devShellDrv;
+}

From af6bd5b12c532238f403f8c1f4758e350e61c871 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 6 Sep 2024 18:34:38 +0200
Subject: [PATCH 14/18] chore: add maintenance just recipe

---
 justfile | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/justfile b/justfile
index b54bda6..10878d9 100644
--- a/justfile
+++ b/justfile
@@ -1,7 +1,9 @@
 set positional-arguments
 set shell := ["bash", "-cue"]
+image := "ghcr.io/sdsc-ordes/fuzon"
 root := justfile_directory()
 
+## build
 
 # build all packages
 build *args:
@@ -20,12 +22,16 @@ maturin-dev *args:
   --uv \
   {{args}}
 
+## development
+
+# enter nix devshell
 develop-nix *args:
   cd {{root}} \
     && cmd=("$@") \
     && { [ -n "${cmd:-}" ] || cmd=("zsh"); } \
     && nix develop ./tools/nix#default --command "${cmd[@]}"
 
+# enter development container
 develop-docker:
   docker run \
     --user 1000:1000 \
@@ -34,13 +40,18 @@ develop-docker:
     --mount type=bind,source="$(pwd)",target=/build/work \
     {{image}}:dev
 
-# maintenance
+## maintenance
 
-image-build:
+# build images
+docker-build:
   nix build -L "./tools/nix#image.dev" --out-link "target/image.dev" \
     && docker load < "build/image.dev"
   nix build -L "./tools/nix#image.fuzon" --out-link "target/image.fuzon" \
     && docker load < "build/image.fuzon"
 
+# push images
+docker-push: docker-build
+  docker push {{image}}:dev
+  docker push {{image}}:fuzon
 
 

From e7934098857b5d8b70231058bb42916c071ef845 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Tue, 10 Sep 2024 15:32:49 +0200
Subject: [PATCH 15/18] fix(just): image file path

---
 justfile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/justfile b/justfile
index 10878d9..4c16291 100644
--- a/justfile
+++ b/justfile
@@ -44,10 +44,10 @@ develop-docker:
 
 # build images
 docker-build:
-  nix build -L "./tools/nix#image.dev" --out-link "target/image.dev" \
-    && docker load < "build/image.dev"
-  nix build -L "./tools/nix#image.fuzon" --out-link "target/image.fuzon" \
-    && docker load < "build/image.fuzon"
+  nix build -L "./tools/nix#images.dev" --out-link "target/image.dev" \
+    && docker load < "target/image.dev"
+  nix build -L "./tools/nix#images.fuzon" --out-link "target/image.fuzon" \
+    && docker load < "target/image.fuzon"
 
 # push images
 docker-push: docker-build

From b253aca7d5ce302bbe6179c6481a33501d38cf8d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gabriel=20N=C3=BCtzi?= <gnuetzi@gmail.com>
Date: Thu, 12 Sep 2024 17:19:24 +0200
Subject: [PATCH 16/18] chore: Nix fixes (#12)

* chore: nix builds now but wont find python

* fix: pass rootSrc to derivation `fuzon`

* fix: correct `python312` dependencies
---
 .gitignore                       |   14 +-
 Cargo.lock                       | 1687 ++++++++++++++++++++++++++++++
 justfile                         |   24 +-
 tools/nix/flake.nix              |   80 +-
 tools/nix/pkgs/fuzon.nix         |   32 -
 tools/nix/pkgs/fuzon/default.nix |   41 +
 6 files changed, 1781 insertions(+), 97 deletions(-)
 create mode 100644 Cargo.lock
 delete mode 100644 tools/nix/pkgs/fuzon.nix
 create mode 100644 tools/nix/pkgs/fuzon/default.nix

diff --git a/.gitignore b/.gitignore
index 70a6345..2faa1fd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+.direnv
+package
+
 # Generated by Cargo
 # will have compiled files and executables
 debug/
@@ -5,23 +8,12 @@ target/
 __pycache__/
 *.so
 
-# Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
-# More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
-Cargo.lock
-
 # These are backup files generated by rustfmt
 **/*.rs.bk
 
-# MSVC Windows builds of rustc generate these, which store debugging information
-*.pdb
-
 # RustRover
 #  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
-
-# Added by cargo
-
-/target
diff --git a/Cargo.lock b/Cargo.lock
new file mode 100644
index 0000000..ccaa4e1
--- /dev/null
+++ b/Cargo.lock
@@ -0,0 +1,1687 @@
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+# It is not intended for manual editing.
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+
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diff --git a/justfile b/justfile
index 4c16291..0cf8434 100644
--- a/justfile
+++ b/justfile
@@ -3,9 +3,9 @@ set shell := ["bash", "-cue"]
 image := "ghcr.io/sdsc-ordes/fuzon"
 root := justfile_directory()
 
-## build
+## Build
 
-# build all packages
+# Build all packages.
 build *args:
   cargo build \
     --manifest-path fuzon/Cargo.toml \
@@ -15,23 +15,27 @@ build *args:
     --release \
     {{args}}
 
-# install editable python package
+# Install editable python package.
 maturin-dev *args:
   maturin develop \
   --manifest-path pyfuzon/Cargo.toml \
   --uv \
   {{args}}
 
-## development
+package-nix *args:
+    cd {{root}} && \
+    nix build "./tools/nix#fuzon" -o "package/fuzon" {{args}}
 
-# enter nix devshell
+## Development
+
+# Enter nix devshell.
 develop-nix *args:
   cd {{root}} \
     && cmd=("$@") \
     && { [ -n "${cmd:-}" ] || cmd=("zsh"); } \
     && nix develop ./tools/nix#default --command "${cmd[@]}"
 
-# enter development container
+# Enter development container
 develop-docker:
   docker run \
     --user 1000:1000 \
@@ -40,18 +44,16 @@ develop-docker:
     --mount type=bind,source="$(pwd)",target=/build/work \
     {{image}}:dev
 
-## maintenance
+## Maintenance
 
-# build images
+# Build images.
 docker-build:
   nix build -L "./tools/nix#images.dev" --out-link "target/image.dev" \
     && docker load < "target/image.dev"
   nix build -L "./tools/nix#images.fuzon" --out-link "target/image.fuzon" \
     && docker load < "target/image.fuzon"
 
-# push images
+# Push images.
 docker-push: docker-build
   docker push {{image}}:dev
   docker push {{image}}:fuzon
-
-
diff --git a/tools/nix/flake.nix b/tools/nix/flake.nix
index 64bafc7..a3f5eb6 100644
--- a/tools/nix/flake.nix
+++ b/tools/nix/flake.nix
@@ -36,25 +36,23 @@
   };
 
   outputs = {
+    self,
     nixpkgs,
     flake-utils,
     rust-overlay,
     ...
-  }: let
-    # This is string (without toString it would be a `path` which is put into the store)
-    rootDir = toString ./. + "../../..";
-    python = nixpkgs.python312;
-  in
+  }:
     flake-utils.lib.eachDefaultSystem
     # Creates an attribute map `{ devShells.<system>.default = ...}`
     # by calling this function:
     (
       system: let
+        rootSrc = ./../..;
+
         overlays = [(import rust-overlay)];
 
         # Import nixpkgs and load it into pkgs.
         # Overlay the rust toolchain
-        lib = nixpkgs.lib;
         pkgs = import nixpkgs {
           inherit system overlays;
         };
@@ -63,7 +61,7 @@
         rustToolchain = pkgs.pkgsBuildHost.rust-bin.fromRustupToolchainFile ../../rust-toolchain.toml;
 
         # Things needed only at compile-time.
-        nativeBuildInputsBasic = with pkgs; [
+        basic-deps = with pkgs; [
           maturin
           findutils
           coreutils
@@ -75,59 +73,55 @@
         ];
 
         # Things needed only at compile-time.
-        nativeBuildInputsDev = with pkgs; [
+        general-deps = [
           rustToolchain
-          cargo-watch
-          just
+          pkgs.cargo-watch
+          pkgs.just
 
-          skopeo
-          dasel
+          pkgs.skopeo
+          pkgs.dasel
+          pkgs.python313
         ];
 
-        benchInputs = with pkgs; [
+        benchmark-deps = with pkgs; [
           hyperfine
           heaptrack
         ];
 
-        # Things needed at runtime.
-        buildInputs = [];
-
         # The package of this CLI tool.
         # The global version for fuzon.
         # This is gonna get tooled later.
-        fuzon = (import ./pkgs/fuzon.nix) {
-          inherit rootDir rustToolchain pkgs lib;
+        fuzon = pkgs.callPackage ./pkgs/fuzon {
+          inherit rootSrc;
+          inherit rustToolchain;
         };
-      in
-        with pkgs; rec {
-          devShells = {
-            default = mkShell {
-              inherit buildInputs;
-              nativeBuildInputs = nativeBuildInputsBasic ++ nativeBuildInputsDev;
-            };
-            bench = mkShell {
-              inherit buildInputs;
-              nativeBuildInputs = nativeBuildInputsBasic 
-                ++ nativeBuildInputsDev
-                ++ benchInputs;
-            };
-
+      in rec {
+        devShells = {
+          default = pkgs.mkShell {
+            packages = basic-deps ++ general-deps;
           };
+          bench = pkgs.mkShell {
+            packages =
+              basic-deps
+              ++ general-deps
+              ++ benchmark-deps;
+          };
+        };
 
-          packages = {
-            fuzon = fuzon;
+        packages = {
+          fuzon = fuzon;
 
-            images = {
-              dev = (import ./images/dev.nix) {
-                inherit pkgs;
-                devShellDrv = devShells.default;
-              };
+          images = {
+            dev = (import ./images/dev.nix) {
+              inherit pkgs;
+              devShellDrv = devShells.default;
+            };
 
-              fuzon = (import ./images/fuzon.nix) {
-                inherit pkgs fuzon;
-              };
+            fuzon = (import ./images/fuzon.nix) {
+              inherit pkgs fuzon;
             };
           };
-        }
+        };
+      }
     );
 }
diff --git a/tools/nix/pkgs/fuzon.nix b/tools/nix/pkgs/fuzon.nix
deleted file mode 100644
index e31dab2..0000000
--- a/tools/nix/pkgs/fuzon.nix
+++ /dev/null
@@ -1,32 +0,0 @@
-{
-  pkgs,
-  lib,
-  rustToolchain,
-  rootDir,
-  ...
-}: let
-  rustPlatform = pkgs.makeRustPlatform {
-    cargo = rustToolchain;
-    rustc = rustToolchain;
-  };
-
-  cargoFile = /. + rootDir + "/fuzon/Cargo.toml";
-  lockFile = /. + rootDir + "/fuzon/Cargo.lock";
-in
-  rustPlatform.buildRustPackage {
-    name = "fuzon";
-    src = /. + rootDir;
-
-    version = (lib.importTOML cargoFile).package.version;
-
-    cargoLock = {
-      inherit lockFile;
-    };
-
-    meta = {
-      description = "A CLI tool to fuzzy search ontology terms by their labels.";
-      homepage = "https://github.com/sdsc-ordes/fuzon";
-      license = lib.licenses.asl20;
-      maintainers = ["gabyx" "cmdoret"];
-    };
-  }
diff --git a/tools/nix/pkgs/fuzon/default.nix b/tools/nix/pkgs/fuzon/default.nix
new file mode 100644
index 0000000..23fd07b
--- /dev/null
+++ b/tools/nix/pkgs/fuzon/default.nix
@@ -0,0 +1,41 @@
+{
+  rootSrc,
+  lib,
+  makeRustPlatform,
+  rustToolchain,
+  python313,
+}: let
+  rustPlatform = makeRustPlatform {
+    cargo = rustToolchain;
+    rustc = rustToolchain;
+  };
+
+  fs = lib.fileset;
+  cargoFile = "${rootSrc}/fuzon/Cargo.toml";
+  lockFile = "${rootSrc}/Cargo.lock";
+in
+  (rustPlatform.buildRustPackage
+    {
+      name = "fuzon";
+
+      src = fs.toSource {
+        root = rootSrc;
+        fileset = fs.gitTracked rootSrc;
+      };
+
+      version = (lib.importTOML cargoFile).package.version;
+
+      cargoLock = {
+        inherit lockFile;
+      };
+
+      meta = {
+        description = "A CLI tool to fuzzy search ontology terms by their labels.";
+        homepage = "https://github.com/sdsc-ordes/fuzon";
+        license = lib.licenses.asl20;
+        maintainers = ["gabyx" "cmdoret"];
+      };
+    })
+  .overrideAttrs (finalAttrs: prevAttrs: {
+    nativeBuildInputs = prevAttrs.nativeBuildInputs ++ [python313];
+  })

From 34f44508725cabf5d01a13fdb2b7adfd6f7955ab Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 13 Sep 2024 15:25:26 +0200
Subject: [PATCH 17/18] docs(readme): update dev instructions

---
 README.md | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 14f1705..73a13a8 100644
--- a/README.md
+++ b/README.md
@@ -56,5 +56,26 @@ A nix dev shell with all build dependencies is provided.
 Assuming just and nix are installed on the machine, you can enter the shell with:
 
 ```shell
-just nix-develop
+just develop-nix
 ```
+
+Alternatively, docker can be used as a development shell:
+
+```shell
+just develop-docker
+```
+
+Once inside a development shell, the python+rust packages can be built with:
+
+```shell
+just build
+```
+
+Or the python bindings can be installed in editable mode using:
+
+```shell
+just maturin-dev
+# pyfuzon now available in python shells
+```
+
+

From fdeafff392a448e7e8781fbf6820abc4726c8272 Mon Sep 17 00:00:00 2001
From: cmdoret <cyril.mattheydoret@gmail.com>
Date: Fri, 13 Sep 2024 15:25:38 +0200
Subject: [PATCH 18/18] chore(just): fix docker mount path

---
 justfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/justfile b/justfile
index 0cf8434..d317502 100644
--- a/justfile
+++ b/justfile
@@ -41,7 +41,7 @@ develop-docker:
     --user 1000:1000 \
     -it \
     -w "/build/workspace" \
-    --mount type=bind,source="$(pwd)",target=/build/work \
+    --mount type=bind,source="$(pwd)",target=/build/workspace \
     {{image}}:dev
 
 ## Maintenance