diff --git a/.claude/agents/replication-coder.md b/.claude/agents/replication-coder.md
index 2a9d6dc..e191b32 100644
--- a/.claude/agents/replication-coder.md
+++ b/.claude/agents/replication-coder.md
@@ -27,11 +27,11 @@ The pipeline must run end-to-end via `snakemake --cores 1` on a fresh checkout.
 3. **Port the analysis** notebook by notebook, in order (01 → 02 → 03 → 04). For each:
    - Read existing notebook content (some may be partial scaffolds).
    - Replace placeholders with real code.
-   - Update `environment.yml` with every new import — see `docs/cicd-conventions.md` § environment.yml is the single source of truth.
+   - Update `pixi.toml` with every new import (then `pixi install` to refresh `pixi.lock`; commit both) — see `docs/cicd-conventions.md` § pixi.toml is the single source of truth.
    - Update the Snakefile rules with the actual file paths.
 4. **Test before claiming done.** See `docs/verify-before-drafting.md` § Test before claiming ready.
-   - Run `snakemake --cores 1 -n` (dry run) to verify the DAG.
-   - Run the notebook(s) end-to-end via `mamba run -n <env> jupytext --to notebook --execute notebooks/0X_….py`.
+   - Run `pixi run snakemake --cores 1 -n` (dry run) to verify the DAG.
+   - Run the notebook(s) end-to-end via `pixi run jupytext --to notebook --execute notebooks/0X_….py`.
    - If you can't run something, mark it explicitly as untested in the conversation.
 
 ## Anti-patterns
@@ -44,4 +44,4 @@ The pipeline must run end-to-end via `snakemake --cores 1` on a fresh checkout.
 
 ## Output
 
-Updated notebook files in `notebooks/`, `environment.yml`, `Snakefile`. Tell the user what runs, what's untested, what you deviated from in the original paper, and what additional credentials / data DOIs they need to set up.
+Updated notebook files in `notebooks/`, `pixi.toml` (+ regenerated `pixi.lock`), `Snakefile`. Tell the user what runs, what's untested, what you deviated from in the original paper, and what additional credentials / data DOIs they need to set up.
diff --git a/.claude/settings.json b/.claude/settings.json
index ae5008a..6270366 100644
--- a/.claude/settings.json
+++ b/.claude/settings.json
@@ -91,6 +91,7 @@
       "Bash(python *)",
       "Bash(python3 *)",
       "Bash(pip *)",
+      "Bash(pixi *)",
       "Bash(mamba *)",
       "Bash(micromamba *)",
       "Bash(conda *)",
diff --git a/.claude/skills/import-from-nanopub/SKILL.md b/.claude/skills/import-from-nanopub/SKILL.md
index bedc29f..998bace 100644
--- a/.claude/skills/import-from-nanopub/SKILL.md
+++ b/.claude/skills/import-from-nanopub/SKILL.md
@@ -67,7 +67,7 @@ What this does, in two layers:
 
 - Scans each Outcome / Research Software nanopub for a `hasOutcomeRepository` URI (which may be either a GitHub URL or a Zenodo DOI — both are handled; Zenodo DOIs are resolved to GitHub URLs via Zenodo's `related_identifiers` API).
 - **`git clone`s each sibling repository** into `--siblings-dir` (default `../`, matching the convention of keeping related replication repos as filesystem siblings).
-- Copies a curated set of starter files from the first cloned sibling into `_template_from_prior/` (`--staging-dir`): `environment.yml`, `Snakefile`, `notebooks/01_data_download.py`, `notebooks/02_data_clean.py`, `Dockerfile`. Each file gets a provenance header.
+- Copies a curated set of starter files from the first cloned sibling into `_template_from_prior/` (`--staging-dir`): `pixi.toml`, `pixi.lock`, `Snakefile`, `notebooks/01_data_download.py`, `notebooks/02_data_clean.py`, `Dockerfile`. Each file gets a provenance header.
 - Writes `nanopubs/imported/SETUP_INHERITED.md` documenting which sibling URLs were resolved, where they were cloned, which files were staged, and what to do with them.
 
 To disable the infrastructure layer (claim-only import), pass `--no-inherit`. To skip cloning but still attempt inheritance from already-present sibling clones, pass `--no-clone-siblings`.
@@ -191,7 +191,7 @@ After `CHAIN_SUMMARY.md` is written, tell the user:
 
 If `SETUP_INHERITED.md` reports that files were copied to `_template_from_prior/`, also tell the user:
 
-> *"The infrastructure-layer inheritance has staged `<N>` starter files at `_template_from_prior/`, copied from the canonical sibling chain. These include `environment.yml`, `Snakefile`, and `notebooks/01_data_download.py` — read the SETUP_INHERITED.md table for the full list and provenance. **Review each staged file, merge with your own at the corresponding path, then delete `_template_from_prior/`.** This staging directory is a one-shot reference area, NOT durable repo state. Do not commit it."*
+> *"The infrastructure-layer inheritance has staged `<N>` starter files at `_template_from_prior/`, copied from the canonical sibling chain. These include `pixi.toml`, `pixi.lock`, `Snakefile`, and `notebooks/01_data_download.py` — read the SETUP_INHERITED.md table for the full list and provenance. **Review each staged file, merge with your own at the corresponding path, then delete `_template_from_prior/`.** This staging directory is a one-shot reference area, NOT durable repo state. Do not commit it."*
 >
 > *If you opted out of cloning (`--no-clone-siblings`) or no `hasOutcomeRepository` URIs were found in the imported nanopubs, the staging area is empty and only the resolved URLs appear in `SETUP_INHERITED.md` for your reference.*
 
diff --git a/.claude/skills/init-template/SKILL.md b/.claude/skills/init-template/SKILL.md
index 846aed2..cc63a3a 100644
--- a/.claude/skills/init-template/SKILL.md
+++ b/.claude/skills/init-template/SKILL.md
@@ -138,9 +138,9 @@ python3 scripts/import-nanopub-chain.py "<PRIOR_CHAIN_URI>"
 This single command does both layers in one pass:
 
 - **Claim layer**: SPARQL-walks the citation graph from the entry URI, fetches every reachable nanopub, caches each TriG to `nanopubs/imported/trig/<RA-id>.trig`, writes `nanopubs/imported/constellation.json` + `cited_papers.txt`.
-- **Infrastructure layer**: resolves each Outcome / Research Software nanopub's `hasOutcomeRepository` URI (GitHub URLs handled directly, Zenodo DOIs resolved via the Zenodo REST API's `related_identifiers`), `git clone`s each sibling repo into `../`, copies starter files (`environment.yml`, `Snakefile`, `notebooks/01_data_download.py`, `02_data_clean.py`, `Dockerfile`) from the canonical sibling into `_template_from_prior/` with provenance headers, and writes `nanopubs/imported/SETUP_INHERITED.md`.
+- **Infrastructure layer**: resolves each Outcome / Research Software nanopub's `hasOutcomeRepository` URI (GitHub URLs handled directly, Zenodo DOIs resolved via the Zenodo REST API's `related_identifiers`), `git clone`s each sibling repo into `../`, copies starter files (`pixi.toml`, `pixi.lock`, `Snakefile`, `notebooks/01_data_download.py`, `02_data_clean.py`, `Dockerfile`) from the canonical sibling into `_template_from_prior/` with provenance headers, and writes `nanopubs/imported/SETUP_INHERITED.md`.
 
-Network access is required. The script depends on `rdflib` (already in the conda env spec).
+Network access is required. The script depends on `rdflib` (already in the pixi env spec).
 
 ### Step 9b — Generate the claim-layer summary
 
diff --git a/.claude/skills/replication-study/SKILL.md b/.claude/skills/replication-study/SKILL.md
index a05b79e..2157675 100644
--- a/.claude/skills/replication-study/SKILL.md
+++ b/.claude/skills/replication-study/SKILL.md
@@ -33,8 +33,8 @@ For each phase, dispatch to the right specialist or guide the user manually:
 |---|---|---|
 | **0 Bootstrap** | Run `/init-template`. Drop paper PDF in `paper/`. | — |
 | **1 Paper analysis** | Use the `paper-analyst` agent. Output: `nanopubs/drafts/00_paper_summary.md` + `nanopubs/drafts/01_quote.md` Quoted Text. | `Agent({subagent_type: "paper-analyst"})` |
-| **2 Code & data port** | Use the `replication-coder` agent. Update `environment.yml`, notebooks, Snakefile. | `Agent({subagent_type: "replication-coder"})` |
-| **3 Local results** | Run `snakemake --cores 1`. Compare headline number to paper. Write `nanopubs/drafts/05_outcome.md` placeholders. | manual |
+| **2 Code & data port** | Use the `replication-coder` agent. Update `pixi.toml` (+ `pixi.lock`), notebooks, Snakefile. | `Agent({subagent_type: "replication-coder"})` |
+| **3 Local results** | Run `pixi run snakemake --cores 1`. Compare headline number to paper. Write `nanopubs/drafts/05_outcome.md` placeholders. | manual |
 | **4 Release** | Run `docs/fair4rs-checklist.md` pre-release checklist. Cut a `gh release` with a Zenodo-formatted body. | manual |
 | **5 FORRT chain** | Use the `nanopub-drafter` agent for each step. User publishes each draft on platform.sciencelive4all.org and pastes the URI into `nanopubs/PUBLISHED.md`. | `Agent({subagent_type: "nanopub-drafter"})` ×6 |
 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d2e6b1a..51d9f83 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,24 +19,25 @@ jobs:
       - name: Skip CI if template has not been initialised or notebooks are scaffolds
         id: guard
         run: |
-          if grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' 2>/dev/null | grep -v '^./.claude/skills/init-template/' | head -1 > /dev/null; then
+          placeholder_files=$(grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' --include='*.toml' 2>/dev/null | grep -v 'claude/skills/init-template/' || true)
+          scaffold_files=$(grep -lE 'raise NotImplementedError|"<dataset-name>"|# Example skeleton — adapt' notebooks/*.py 2>/dev/null || true)
+          if [ -n "$placeholder_files" ]; then
             echo "::notice::Template placeholders detected ({{...}} tokens). Run /init-template inside Claude Code (or substitute manually) before CI runs meaningfully. Skipping the rest of this workflow."
             echo "skip=true" >> "$GITHUB_OUTPUT"
-          elif grep -lE 'raise NotImplementedError|"<dataset-name>"|# Example skeleton — adapt' notebooks/*.py 2>/dev/null | head -1 > /dev/null; then
+          elif [ -n "$scaffold_files" ]; then
             echo "::notice::Notebooks are still in scaffold state — replace placeholders in notebooks/*.py with your actual replication code (Phase 2). The Snakefile rule outputs will not be produced until then. Skipping pipeline run."
             echo "skip=true" >> "$GITHUB_OUTPUT"
           else
             echo "skip=false" >> "$GITHUB_OUTPUT"
           fi
 
-      - name: Set up Micromamba
+      - name: Set up pixi
         if: steps.guard.outputs.skip != 'true'
-        uses: mamba-org/setup-micromamba@v3
+        uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          environment-file: environment.yml
-          environment-name: ${{ github.event.repository.name }}
-          init-shell: bash
-          cache-environment: true
+          pixi-version: v0.68.1
+          locked: true
+          cache: true
 
       # ----- credentials (uncomment + add the matching GitHub secret) -----
       #
@@ -64,8 +65,7 @@ jobs:
 
       - name: Run pipeline
         if: steps.guard.outputs.skip != 'true'
-        shell: micromamba-shell {0}
-        run: snakemake --cores 1
+        run: pixi run snakemake --cores 1
 
       - name: Upload results
         if: always() && steps.guard.outputs.skip != 'true'
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 2eefa9e..224afe5 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -23,7 +23,8 @@ jobs:
       - name: Skip if template has not been initialised
         id: guard
         run: |
-          if grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' 2>/dev/null | grep -v '^./.claude/skills/init-template/' | head -1 > /dev/null; then
+          placeholder_files=$(grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' --include='*.toml' 2>/dev/null | grep -v 'claude/skills/init-template/' || true)
+          if [ -n "$placeholder_files" ]; then
             echo "::notice::Template placeholders detected ({{...}} tokens). Run /init-template before releasing. Skipping Docker build."
             echo "skip=true" >> "$GITHUB_OUTPUT"
           else
diff --git a/.github/workflows/jupyter-book.yml b/.github/workflows/jupyter-book.yml
index 6f00d51..33c9460 100644
--- a/.github/workflows/jupyter-book.yml
+++ b/.github/workflows/jupyter-book.yml
@@ -26,7 +26,8 @@ jobs:
       - name: Skip if template has not been initialised
         id: guard
         run: |
-          if grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' 2>/dev/null | grep -v '^./.claude/skills/init-template/' | head -1 > /dev/null; then
+          placeholder_files=$(grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' --include='*.toml' 2>/dev/null | grep -v 'claude/skills/init-template/' || true)
+          if [ -n "$placeholder_files" ]; then
             echo "::notice::Template placeholders detected ({{...}} tokens). Run /init-template inside Claude Code (or substitute manually) before the Jupyter Book builds meaningfully. Skipping."
             echo "skip=true" >> "$GITHUB_OUTPUT"
           else
@@ -39,7 +40,7 @@ jobs:
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          if gh api "repos/${{ github.repository }}/pages" 2>/dev/null | head -1 > /dev/null; then
+          if gh api "repos/${{ github.repository }}/pages" >/dev/null 2>&1; then
             echo "::notice::GitHub Pages is enabled — Jupyter Book will deploy."
             echo "pages_enabled=true" >> "$GITHUB_OUTPUT"
           else
@@ -47,50 +48,39 @@ jobs:
             echo "pages_enabled=false" >> "$GITHUB_OUTPUT"
           fi
 
-      - name: Set up Micromamba
+      - name: Set up pixi
         if: steps.guard.outputs.skip != 'true'
-        uses: mamba-org/setup-micromamba@v3
+        uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          environment-file: environment.yml
-          environment-name: ${{ github.event.repository.name }}
-          init-shell: bash
-          cache-environment: true
+          pixi-version: v0.68.1
+          locked: true
+          cache: true
+          environments: docs
 
       - name: Convert .py notebooks to .ipynb
         if: steps.guard.outputs.skip != 'true'
-        shell: micromamba-shell {0}
         run: |
           for nb in notebooks/*.py; do
-            jupytext --to notebook "$nb"
+            pixi run jupytext --to notebook "$nb"
           done
 
       # Glob, not a hard-coded list — new notebooks are picked up automatically.
       - name: Execute notebooks
         if: steps.guard.outputs.skip != 'true'
-        shell: micromamba-shell {0}
         run: |
           for nb in notebooks/*.ipynb; do
             echo "::group::Executing $nb"
-            jupyter execute --inplace "$nb"
+            pixi run jupyter execute --inplace "$nb"
             echo "::endgroup::"
           done
 
-      - uses: actions/setup-node@v4
-        if: steps.guard.outputs.skip != 'true'
-        with:
-          node-version: 22.x
-
-      - name: Install MyST
-        if: steps.guard.outputs.skip != 'true'
-        run: npm install -g mystmd
-
       - name: Build MyST site
         if: steps.guard.outputs.skip != 'true'
         env:
           # MyST silently ignores `base_url` in myst.yml — only this env var
           # works. See docs/cicd-conventions.md.
           BASE_URL: /${{ github.event.repository.name }}
-        run: myst build --html
+        run: pixi run -e docs myst build --html
 
       - name: Upload pages artifact
         if: steps.guard.outputs.skip != 'true'
diff --git a/.gitignore b/.gitignore
index 83c332b..086f10a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,6 +13,14 @@ __pycache__/
 .venv/
 .pytest_cache/
 
+# Pixi install cache — never committed. pixi.toml + pixi.lock ARE committed
+# (they're the dep manifest + per-platform lockfile); the .pixi/ directory is
+# the per-machine install of the resolved env and is regenerated by `pixi install`.
+.pixi/
+
+# Snakemake run cache (DAG, locks, log files for each invocation)
+.snakemake/
+
 # Environment / OS
 .DS_Store
 .env
diff --git a/CLAUDE.md b/CLAUDE.md
index 70fb08e..a2dbb6c 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -25,7 +25,7 @@ Key FAIR4RS handles in this template:
 
 - **F (Findable)** — Zenodo concept DOI minted at first release; `CITATION.cff` + `codemeta.json` populated; GitHub topics suggested in `README.md`.
 - **A (Accessible)** — public GitHub repo, MIT license, GHCR image, Zenodo archive of the source tarball and (optionally) the Docker image, so the software remains accessible even if GitHub or GHCR disappears.
-- **I (Interoperable)** — `environment.yml` is the single declarative source of truth; standard formats (jupytext `.py` notebooks, parquet/CSV/NetCDF data, OCI Docker image); cross-references to upstream paper DOI, dataset DOIs, and FORRT nanopub URIs use qualified relations.
+- **I (Interoperable)** — `pixi.toml` + `pixi.lock` are the single declarative source of truth (the lockfile pins every package per platform); standard formats (jupytext `.py` notebooks, parquet/CSV/NetCDF data, OCI Docker image); cross-references to upstream paper DOI, dataset DOIs, and FORRT nanopub URIs use qualified relations.
 - **R (Reusable)** — explicit MIT license, detailed provenance via the FORRT chain (every claim traceable to data + method + author ORCID), `CITATION.cff` lists upstream paper as a `references` entry, `codemeta.json` lists `softwareRequirements` and `referencePublication`.
 
 The FORRT nanopublication chain itself is what makes **R1.2 (provenance)** machine-actionable: it does what `CITATION.cff` cannot, by separating *claims about the world* from *facts about the software*, with cryptographically signed nanopubs at each step.
@@ -89,7 +89,7 @@ Exit (either entry point): a complete `nanopubs/drafts/01_quote.md` with verifie
 
 ### Phase 2 — Code & data port
 
-- `environment.yml` lists every dependency the notebooks import (`docs/cicd-conventions.md` § environment.yml is the single source of truth).
+- `pixi.toml` lists every dependency the notebooks import, and `pixi.lock` is regenerated and committed alongside it (`docs/cicd-conventions.md` § pixi.toml is the single source of truth).
 - `notebooks/01_data_download.py` fetches all input data — no manual steps.
 - `notebooks/02_data_clean.py` produces a tidy intermediate dataset.
 - `notebooks/03_analysis.py` reproduces the paper's headline statistic.
@@ -180,7 +180,7 @@ The documents under `docs/` are the load-bearing reference material; reach for t
 | Choose the FORRT Claim type | `docs/claim-type-vocabulary.md` |
 | Write the Quote, Study, or Outcome | `docs/verify-before-drafting.md` |
 | Write a PICO or PCC question | `docs/pico-study-outcome-levels.md` |
-| Touch CI / environment.yml / Dockerfile / myst.yml | `docs/cicd-conventions.md` |
+| Touch CI / pixi.toml / Dockerfile / myst.yml | `docs/cicd-conventions.md` |
 | Cut a release / claim a phase done | `docs/fair4rs-checklist.md` |
 | Update RO-Crate metadata after adding artefacts | `docs/ro-crate.md` |
 | Need to retract / supersede / batch-publish a nanopub | `docs/programmatic-nanopubs.md` |
diff --git a/DOMAIN.md b/DOMAIN.md
index 8408177..86c215c 100644
--- a/DOMAIN.md
+++ b/DOMAIN.md
@@ -31,7 +31,7 @@ When the user asks Claude to set up a typical analysis, the default tools to sug
 | Intermediate / archival arrays | `netCDF4` (small ≤2 GB), `zarr` (larger / cloud) | **never `.npz`** — see Data formats convention below |
 | HEALPix-indexed EO archival | EOPF Zarr (Earth Observation Processing Framework profile) | Standardised metadata for HEALPix dim-naming, NESTED ordering, projection. See [`EOPF-DGGS/legacy-converters`](https://github.com/EOPF-DGGS/legacy-converters) for conversion patterns. |
 
-Pin every dependency in `environment.yml` — pangeo dev environments hide missing deps locally and CI then silently fails with empty notebook cells.
+Pin every dependency in `pixi.toml` and commit the regenerated `pixi.lock` — pangeo dev environments hide missing deps locally and CI then silently fails with empty notebook cells.
 
 ## Domain conventions
 
diff --git a/Dockerfile b/Dockerfile
index 68cab11..b6c710c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,19 +1,20 @@
-FROM mambaorg/micromamba:1.5-jammy
+FROM ghcr.io/prefix-dev/pixi:0.68.1
 
 LABEL org.opencontainers.image.source="https://github.com/{{REPO_ORG}}/{{REPO_NAME}}"
 LABEL org.opencontainers.image.description="Replication study container for {{REPO_NAME}}"
 LABEL org.opencontainers.image.licenses="MIT"
 
-COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
-RUN micromamba install -y -n base -f /tmp/environment.yml && \
-    micromamba clean --all --yes
-
 WORKDIR /app
-COPY --chown=$MAMBA_USER:$MAMBA_USER . /app
+
+# Install the pinned environment first (separate from source copy so the lock
+# layer is cached across source-only edits).
+COPY pixi.toml pixi.lock /app/
+RUN pixi install --locked
+
+COPY . /app
 
 # Mount any required credentials at runtime, e.g.:
 #   docker run -v ~/.cdsapirc:/home/mambauser/.cdsapirc {{REPO_NAME}}
 # See data/README.md for per-dataset credential setup.
 
-ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
-CMD ["snakemake", "--cores", "1"]
+CMD ["pixi", "run", "snakemake", "--cores", "1"]
diff --git a/README.md b/README.md
index f62c472..df68d42 100644
--- a/README.md
+++ b/README.md
@@ -22,11 +22,12 @@ This is a self-contained replication of the headline claim of the reference pape
 ```bash
 git clone https://github.com/{{REPO_ORG}}/{{REPO_NAME}}.git
 cd {{REPO_NAME}}
-mamba env create -f environment.yml
-mamba activate {{REPO_NAME}}
-snakemake --cores 1
+pixi install
+pixi run snakemake --cores 1
 ```
 
+(Pixi resolves `pixi.toml` against the per-platform `pixi.lock`, installs the env under `.pixi/`, and provides `pixi run` for any task without needing an `activate` step.)
+
 Or with Docker:
 
 ```bash
@@ -58,7 +59,7 @@ After `/init-template`, do these one-time setup steps to enable the full CI/CD p
 ├── CITATION.cff                # how to cite
 ├── codemeta.json               # software metadata (CodeMeta-2.0)
 ├── ro-crate-metadata.json      # research object packaging (RO-Crate 1.2)
-├── environment.yml             # conda/pip dependencies (single source of truth)
+├── pixi.toml + pixi.lock       # pinned dependencies (single source of truth; lockfile is per-platform)
 ├── Dockerfile                  # container build
 ├── Snakefile                   # pipeline orchestration
 ├── myst.yml + index.md         # Jupyter Book scaffold
@@ -78,8 +79,8 @@ This template bakes in conventions that took multiple replications to discover.
 
 - **FAIR4RS conformance** — see [`docs/fair4rs-checklist.md`](docs/fair4rs-checklist.md) for the principle-by-principle mapping.
 - **Self-contained data downloads** — the first notebook fetches everything; no manual data prep.
-- **`environment.yml` as single source of truth** — local dev, Docker, and CI all use the same pinned versions.
-- **`mamba-org/setup-micromamba@v3`-based CI** — caches the env, runs the pipeline, executes notebooks via a glob.
+- **`pixi.toml` + `pixi.lock` as single source of truth** — local dev, Docker, and CI all install the same per-platform-pinned env.
+- **`prefix-dev/setup-pixi`-based CI** — caches the env, runs the pipeline with `pixi run`, executes notebooks via a glob, fails fast on a stale lockfile.
 - **Jupyter Book deployment** — auto-deploys to GitHub Pages with `BASE_URL` set correctly. (Don't put `base_url` in `myst.yml` — MyST silently ignores it.)
 - **Docker + GHCR + Zenodo image archival** — `release` trigger pushes to GHCR and (optionally) archives to Zenodo for long-term preservation.
 - **RO-Crate packaging** — the entire repo is a navigable Research Object via `ro-crate-metadata.json` (Process Run Crate + Workflow RO-Crate profiles).
diff --git a/docs/cicd-conventions.md b/docs/cicd-conventions.md
index 3e46c26..f5a97e7 100644
--- a/docs/cicd-conventions.md
+++ b/docs/cicd-conventions.md
@@ -1,33 +1,33 @@
 # `docs/cicd-conventions.md` — CI/CD, environment, and Jupyter Book conventions
 
-Hard-won rules for replication repos using `mamba` + `setup-micromamba` + `MyST` + GitHub Actions. Each rule has an associated failure mode that has cost real debugging time in past projects.
+Hard-won rules for replication repos using `pixi` + `prefix-dev/setup-pixi` + `MyST` + GitHub Actions. Each rule has an associated failure mode that has cost real debugging time in past projects.
 
 ---
 
-## environment.yml is the single source of truth
+## `pixi.toml` is the single source of truth
 
-All CI workflows MUST use `mamba-org/setup-micromamba@v3` with the repo's `environment.yml`. Never duplicate dependency lists in manual `pip install` lines in workflow YAML.
+All CI workflows MUST use `prefix-dev/setup-pixi@v0.9.6` with the repo's `pixi.toml` + `pixi.lock`. Never duplicate dependency lists in manual `pip install` lines in workflow YAML.
 
 Pattern:
 
 ```yaml
-- uses: mamba-org/setup-micromamba@v3
+- uses: prefix-dev/setup-pixi@v0.9.6
   with:
-    environment-file: environment.yml
-    environment-name: {{REPO_NAME}}
-    init-shell: bash
-    cache-environment: true
+    pixi-version: v0.68.1
+    locked: true
+    cache: true
 
 - name: Run notebook
-  shell: micromamba-shell {0}
-  run: jupyter execute --inplace notebooks/03_analysis.ipynb
+  run: pixi run jupyter execute --inplace notebooks/03_analysis.ipynb
 ```
 
-The `environment.yml` must include **every** dependency the notebooks import: `nbclient`, `ipykernel`, `pytorch-cpu`, `jupytext`, etc. Local "kitchen-sink" envs (e.g. `pangeo`) hide missing deps because they have everything pre-installed; CI builds strictly from `environment.yml` and silently produces empty notebook cells if anything is missing.
+The `pixi.toml` must include **every** dependency the notebooks import: `nbclient`, `ipykernel`, `pytorch-cpu`, `jupytext`, etc. Local "kitchen-sink" envs (e.g. `pangeo`) hide missing deps because they have everything pre-installed; CI builds strictly from `pixi.lock` and silently produces empty notebook cells if anything is missing.
+
+`pixi.lock` is committed alongside `pixi.toml`. When you edit `pixi.toml`, run `pixi install` locally to refresh the lockfile and commit both files in the same commit. CI runs with `locked: true` so a stale `pixi.lock` fails fast instead of silently re-solving.
 
 ### Failure mode
 
-A previous repo's notebooks 04 and 06 imported `sklearn` but `scikit-learn` wasn't in `environment.yml`. Local execution worked (pangeo has it). CI's Jupyter Book build silently produced empty cells where the sklearn imports failed. The deployed Jupyter Book showed empty figure cells with no error indication. Fix: add `scikit-learn` to `environment.yml`.
+A previous repo's notebooks 04 and 06 imported `sklearn` but `scikit-learn` wasn't in the dep manifest. Local execution worked (pangeo has it). CI's Jupyter Book build silently produced empty cells where the sklearn imports failed. The deployed Jupyter Book showed empty figure cells with no error indication. Fix: add `scikit-learn` to `pixi.toml`, `pixi install`, commit both files.
 
 ### How to audit
 
@@ -37,31 +37,15 @@ Cross-check before pushing:
 grep -h "^import\|^from" notebooks/*.py | sort -u
 ```
 
-…and verify every external module appears in `environment.yml`.
+…and verify every external module appears in `pixi.toml` (top-level `[dependencies]` or under a `[feature.*.dependencies]` table).
 
 ---
 
-## snakemake on `setup-micromamba@v3` — install via pip
-
-On GitHub Actions using `mamba-org/setup-micromamba@v3`, both `snakemake` and `snakemake-minimal` fail to solve from conda-forge with:
-
-```
-error    libmamba Could not solve for environment specs
-    └─ snakemake =* * does not exist (perhaps a typo or a missing channel).
-```
-
-Other conda-forge packages in the same environment solve fine. Workaround: install `snakemake` via the pip section of `environment.yml`:
+## Channels: conda-forge first, bioconda for snakemake
 
-```yaml
-dependencies:
-  - python=3.12
-  # ... conda deps ...
-  - pip
-  - pip:
-    - snakemake
-```
+`pixi.toml` declares channels with `conda-forge` first and `bioconda` second. Conda-forge handles the scientific stack; `bioconda` hosts `snakemake` (and the wider rule-engine ecosystem) — it is not in conda-forge. Pixi handles multi-channel solves cleanly; no per-package pinning to channel is needed.
 
-This bypasses the conda solver and installs from PyPI in the same env. Apply the same workaround to any other conda-forge package that hits the `=* *` error.
+If a notebook needs a pip-only package (e.g. `polytope-client`, `pygbif`'s pre-release), add a `[pypi-dependencies]` block. Pixi resolves PyPI deps against the conda env's Python — no parallel virtualenv.
 
 ---
 
@@ -73,11 +57,13 @@ For Jupyter Book to deploy correctly to GitHub Pages, the `BASE_URL` env var mus
 - name: Build MyST site
   env:
     BASE_URL: /${{ github.event.repository.name }}
-  run: myst build --html
+  run: pixi run -e docs myst build --html
 ```
 
 **Do NOT set `base_url` in `myst.yml`** — MyST silently ignores the key (with a warning if you look at the build log carefully). Without `BASE_URL`, the deployed site shows a "Site not loading correctly? This may be due to an incorrect BASE_URL configuration" error.
 
+MyST itself is installed as a conda-forge package in the `docs` pixi feature (`mystmd`), so the workflow doesn't need a separate `setup-node` + `npm install -g mystmd` step — `pixi run -e docs myst …` picks up the env-installed binary.
+
 ---
 
 ## `myst.yml` TOC references `.ipynb`, not `.py`
@@ -95,10 +81,9 @@ The CI workflow converts `.py` to `.ipynb` with `jupytext` before MyST builds:
 
 ```yaml
 - name: Convert .py notebooks to .ipynb
-  shell: micromamba-shell {0}
   run: |
     for nb in notebooks/*.py; do
-      jupytext --to notebook "$nb"
+      pixi run jupytext --to notebook "$nb"
     done
 ```
 
@@ -110,11 +95,10 @@ Without `--inplace`, the executed notebook outputs are not written back to the `
 
 ```yaml
 - name: Execute notebooks
-  shell: micromamba-shell {0}
   run: |
     for nb in notebooks/*.ipynb; do
       echo "::group::Executing $nb"
-      jupyter execute --inplace "$nb"
+      pixi run jupyter execute --inplace "$nb"
       echo "::endgroup::"
     done
 ```
@@ -194,7 +178,7 @@ If an analysis takes more than ~5 minutes:
 4. Check results when the user asks or in the next conversation.
 
 ```bash
-nohup python notebooks/03_analysis.py > results/logs/analysis.log 2>&1 &
+nohup pixi run python notebooks/03_analysis.py > results/logs/analysis.log 2>&1 &
 echo "Started; tail -f results/logs/analysis.log"
 ```
 
@@ -225,9 +209,12 @@ The secret is a base64-encoded INI file. Generate it locally with `base64 < ~/.c
 Before pushing a release-relevant change, audit:
 
 ```bash
-# Every notebook import is in environment.yml
+# Every notebook import is in pixi.toml
 grep -h "^import\|^from" notebooks/*.py | sort -u
 
+# pixi.lock is fresh (no diff after a clean install)
+pixi install --locked && git diff --exit-code pixi.lock
+
 # myst.yml TOC references .ipynb (not .py)
 grep "\.py" myst.yml
 
diff --git a/docs/domain-flavours/_template.md b/docs/domain-flavours/_template.md
index dd085ce..4cc2546 100644
--- a/docs/domain-flavours/_template.md
+++ b/docs/domain-flavours/_template.md
@@ -15,7 +15,7 @@ When the user asks Claude to set up a typical analysis, the default tools to sug
 | <e.g. tabular data> | <e.g. `pandas`> | <one-line note> |
 | ... | ... | ... |
 
-Pin every dependency in `environment.yml`.
+Pin every dependency in `pixi.toml` and commit the regenerated `pixi.lock`.
 
 ## Domain conventions
 
diff --git a/docs/domain-flavours/biodiversity-earth-observation.md b/docs/domain-flavours/biodiversity-earth-observation.md
index 04cc99d..1b65461 100644
--- a/docs/domain-flavours/biodiversity-earth-observation.md
+++ b/docs/domain-flavours/biodiversity-earth-observation.md
@@ -28,7 +28,7 @@ When the user asks Claude to set up a typical analysis, the default tools to sug
 | Raster / vector I/O | `rasterio`, `geopandas` | |
 | Scattering on the sphere | `foscat>=2026.4.1` | upstream PyPI; CPU auto-detection |
 
-Pin every dependency in `environment.yml` — pangeo dev environments hide missing deps locally and CI then silently fails with empty notebook cells.
+Pin every dependency in `pixi.toml` and commit the regenerated `pixi.lock` — pangeo dev environments hide missing deps locally and CI then silently fails with empty notebook cells.
 
 ## Domain conventions
 
diff --git a/docs/fair4rs-checklist.md b/docs/fair4rs-checklist.md
index 55254d6..40f0552 100644
--- a/docs/fair4rs-checklist.md
+++ b/docs/fair4rs-checklist.md
@@ -86,8 +86,8 @@ Public release artefacts are anonymous-accessible. Private upstream data sources
 
 | Where | Evidence |
 |---|---|
-| `environment.yml` declarative dependency manifest | conda/pip standard format. |
-| `Dockerfile` based on `mambaorg/micromamba` | OCI-compliant container. |
+| `pixi.toml` + `pixi.lock` declarative dependency manifest | TOML manifest + per-platform lockfile pinning every package to an exact build hash; conda + PyPI sources. |
+| `Dockerfile` based on `ghcr.io/prefix-dev/pixi` | OCI-compliant container; image installs from `pixi.lock` so the container env is byte-identical to local + CI. |
 | Notebook outputs | NetCDF, parquet, CSV, GeoTIFF — all open, community-standard formats. |
 | Jupyter Book + jupytext `.py` source-of-truth | open notebook formats; `.py` is round-trippable to `.ipynb`. |
 
@@ -139,7 +139,7 @@ A reader who finds this software via its Zenodo DOI can follow the references to
 
 | Where | Evidence |
 |---|---|
-| `environment.yml` and `codemeta.json` `softwareRequirements` | declared upstream dependencies. |
+| `pixi.toml` (+ `pixi.lock`) and `codemeta.json` `softwareRequirements` | declared upstream dependencies; the lockfile additionally pins each upstream package to an exact build hash. |
 | Research Software nanopub for upstream tools (when applicable) | the upstream library (e.g. `foscat`, `planktonclas`) gets its own Research Software nanopub that the FORRT Outcome cites. |
 
 If your replication's reusable artefact is an upstream library (not just a one-off demo), publish a separate Research Software nanopub for the upstream tool. See `CLAUDE.md` § Layered architecture: FORRT vs Research Software, and `docs/forrt-form-fields.md` § Research Software.
@@ -160,8 +160,8 @@ Run this list before cutting any GitHub release:
 
 - [ ] `CITATION.cff` `version` and `date-released` updated.
 - [ ] `codemeta.json` `version` and `dateModified` updated.
-- [ ] All `{{...}}` placeholder tokens substituted (run `grep -r '{{' . --include='*.md' --include='*.yml' --include='*.json' --include='*.cff'`).
-- [ ] `environment.yml` lists every notebook import (`grep -h "^import\|^from" notebooks/*.py | sort -u`).
+- [ ] All `{{...}}` placeholder tokens substituted (run `grep -r '{{' . --include='*.md' --include='*.yml' --include='*.json' --include='*.cff' --include='*.toml'`).
+- [ ] `pixi.toml` lists every notebook import (`grep -h "^import\|^from" notebooks/*.py | sort -u`); `pixi.lock` is fresh (`pixi install --locked && git diff --exit-code pixi.lock`).
 - [ ] `LICENSE` carries the right author and year.
 - [ ] Release notes follow the Zenodo-description format (`docs/cicd-conventions.md` § Release notes are Zenodo descriptions).
 - [ ] If this is the first release: `CITATION.cff` `doi` field is left as `{{ZENODO_DOI}}` (the integration mints it on release; update afterwards).
diff --git a/docs/nanopub-chain-discovery.md b/docs/nanopub-chain-discovery.md
index 689e3e8..ca35be7 100644
--- a/docs/nanopub-chain-discovery.md
+++ b/docs/nanopub-chain-discovery.md
@@ -97,7 +97,7 @@ Add the URI to `CITATION.cff`; let the cache live and die in `nanopubs/imported/
 
 The inherited files are deliberately staged to `_template_from_prior/` rather than the new repo's actual locations:
 
-- `_template_from_prior/environment.yml` — pinned dependencies from the canonical sibling
+- `_template_from_prior/pixi.toml` + `_template_from_prior/pixi.lock` — pinned dependencies and per-platform lockfile from the canonical sibling
 - `_template_from_prior/Snakefile` — workflow scaffold
 - `_template_from_prior/notebooks/01_data_download.py` — data-access patterns (GBIF pre-minted-DOI, Polytope for DestinE, Figshare for CRU TS, etc.)
 - `_template_from_prior/notebooks/02_data_clean.py` — cleaning patterns
diff --git a/docs/ro-crate.md b/docs/ro-crate.md
index a3e7459..af3ed31 100644
--- a/docs/ro-crate.md
+++ b/docs/ro-crate.md
@@ -20,7 +20,7 @@ The default `ro-crate-metadata.json` lists:
 - **Workflow** — `Snakefile` typed as `SoftwareSourceCode` + `ComputationalWorkflow`, with declared inputs and outputs.
 - **Notebooks** — each `notebooks/*.py` typed as `SoftwareSourceCode` + `Notebook`.
 - **Datasets** — `paper/`, `data/`, `results/`, `figures/` typed as `Dataset` with descriptions.
-- **Configuration files** — `environment.yml`, `Dockerfile` typed as `ConfigurationFile`.
+- **Configuration files** — `pixi.toml`, `pixi.lock`, `Dockerfile` typed as `ConfigurationFile`.
 - **Citation** — back-link to the original paper DOI as `ScholarlyArticle`.
 - **Nanopub registry** — `nanopubs/PUBLISHED.md` typed as `TextObject` with description pointing to the FORRT chain.
 
diff --git a/docs/verify-before-drafting.md b/docs/verify-before-drafting.md
index c81a308..bd698f3 100644
--- a/docs/verify-before-drafting.md
+++ b/docs/verify-before-drafting.md
@@ -66,8 +66,8 @@ When writing notebook or script code that uses unfamiliar APIs, **run it before
 
 ### Procedure
 
-- Try to run the code locally (`mamba env create -f environment.yml` then `mamba run -n {{REPO_NAME}} python notebooks/01_data_download.py` — the env name comes from `environment.yml`).
-- If a needed dep is missing, say "I haven't run this — would need to add `X` to `environment.yml`. Run it first?"
+- Try to run the code locally (`pixi install` then `pixi run python notebooks/01_data_download.py` — pixi reads `pixi.toml` and uses the lockfile to install a per-platform environment under `.pixi/`).
+- If a needed dep is missing, say "I haven't run this — would need to add `X` to `pixi.toml`. Run it first?"
 - **Never describe untested code as "works" or "ready"** — say "written, untested" or "written, runs in the Docker container per the API docs, not yet executed."
 - This applies especially to code using libraries with version-specific APIs (h3 v3 vs v4, rhealpixdggs, dggrid4py, foscat versions).
 
@@ -75,7 +75,7 @@ When writing notebook or script code that uses unfamiliar APIs, **run it before
 
 In a previous DGGS replication, code using `h3` and `rhealpixdggs` was written from API documentation alone, declared "ready to commit", and then the user asked: *"did you test it locally?"* — at which point the answer had to be "no". The code did happen to work, but the right protocol is to test first or be explicit that it is untested.
 
-The cost of testing is small (one `mamba run` invocation). The cost of an incorrectly-claimed "works" is a debugging round-trip and credibility loss.
+The cost of testing is small (one `pixi run` invocation). The cost of an incorrectly-claimed "works" is a debugging round-trip and credibility loss.
 
 ---
 
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 5b6e89c..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-# Single source of truth for the runtime — used by local dev, Docker, and CI.
-# Add every dependency a notebook imports here. Local "kitchen-sink" envs
-# (e.g. pangeo) hide missing deps; CI builds strictly from this file and will
-# silently produce empty notebook cells if anything is missing.
-name: "{{REPO_NAME}}"
-channels:
-  - conda-forge
-dependencies:
-  - python=3.12
-  # --- core scientific stack ---
-  - numpy
-  - pandas>=2.0
-  - xarray>=2024.6
-  - scipy
-  - matplotlib
-  - pyarrow
-  # --- notebook execution + Jupyter Book ---
-  - jupytext
-  - jupyterlab
-  - nbclient
-  - ipykernel
-  # --- replace/extend with the deps your replication needs ---
-  # Examples (uncomment as needed):
-  # - statsmodels             # GLM/GLMM regression
-  # - scikit-learn            # classical ML
-  # - pyproj                  # CRS + map projections
-  # - cartopy                 # geographic plotting
-  # - netcdf4                 # NetCDF I/O — preferred over .npz for arrays (see DOMAIN.md)
-  # - zarr                    # Zarr — preferred for arrays >2 GB or cloud-archived (see DOMAIN.md)
-  # - cdsapi                  # Copernicus Climate Data Store
-  # - copernicusmarine        # Copernicus Marine Service
-  # - healpix-geo             # HEALPix on geo data — preferred (use nest=True — see DOMAIN.md)
-  # - healpy                  # HEALPix on pure-sphere (astrophysics) only
-  # - rasterio                # raster I/O
-  # - geopandas               # vector I/O
-  # - dask                    # out-of-core / parallel
-  - pip
-  - pip:
-    # snakemake on conda-forge fails to solve under setup-micromamba@v3 —
-    # install via pip. See docs/cicd-conventions.md.
-    - snakemake
-    # Add pip-only deps here, e.g.:
-    # - pygbif
-    # - polytope-client       # Destination Earth Climate DT
-    # - earthkit-data
diff --git a/index.md b/index.md
index d14cb7b..de40503 100644
--- a/index.md
+++ b/index.md
@@ -15,9 +15,8 @@ This repository is a self-contained replication of the headline claim from the r
 ```bash
 git clone https://github.com/{{REPO_ORG}}/{{REPO_NAME}}.git
 cd {{REPO_NAME}}
-mamba env create -f environment.yml
-mamba activate {{REPO_NAME}}
-snakemake --cores 1
+pixi install
+pixi run snakemake --cores 1
 ```
 
 Or with Docker:
diff --git a/notebooks/README.md b/notebooks/README.md
index 279ef59..bb3b93a 100644
--- a/notebooks/README.md
+++ b/notebooks/README.md
@@ -27,7 +27,7 @@ When you add a notebook:
 2. Add it to `myst.yml` TOC as `notebooks/0X_….ipynb` (note: `.ipynb`, not `.py`; MyST cannot process `.py`).
 3. Add a Snakefile rule that wraps it.
 4. The `.github/workflows/jupyter-book.yml` "Execute notebooks" step uses a glob (`notebooks/*.ipynb`), so new notebooks are picked up automatically — no workflow edit needed.
-5. Add every import in the new notebook to `environment.yml`.
+5. Add every import in the new notebook to `pixi.toml`, then `pixi install` and commit the refreshed `pixi.lock`.
 
 ## Anti-patterns
 
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 0000000..9afa028
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,11890 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://conda.anaconda.org/bioconda/
+    options:
+      pypi-prerelease-mode: if-necessary-or-explicit
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.6-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-doc-0.0.4-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py312h4c3975b_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/argparse-dataclass-2.0.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/async-lru-2.3.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.10.1-ha62d5e7_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.2-h8b1a151_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.7.0-h9b893ba_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.13-h4bacb7b_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.26.3-hb18f61d_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.15.2-hc1936db_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.12.2-he6ee468_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.10-h8b1a151_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.38.3-h745e52d_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.747-h41c0014_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.16.2-h206d751_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-identity-cpp-1.13.3-hed0cdb0_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.16.0-hf824e48_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.13.0-ha7a2c86_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h539c000_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.18.0-pyhcf101f3_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.5.0-py312h90b7ffd_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.14.3-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-6.3.0-pyhcf101f3_1.conda
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+  license: MIT
+  license_family: MIT
+  size: 18701
+  timestamp: 1769434732453
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+  license_family: MIT
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+  - python >=3.10
+  - pyyaml >=6.0,<7.0
+  license: MIT
+  license_family: MIT
+  size: 16215
+  timestamp: 1764250734338
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h09e67af_11.conda
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+  license: MPL-2.0
+  license_family: MOZILLA
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+- conda: https://conda.anaconda.org/conda-forge/win-64/zeromq-4.3.5-h3a581c9_11.conda
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+  license: MPL-2.0
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+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
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+  - python
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+  license: Zlib
+  license_family: Other
+  size: 95931
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.2-h8088a28_2.conda
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000..90ee397
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,69 @@
+# Single source of truth for the runtime — used by local dev, Docker, and CI.
+# Add every dependency a notebook imports here. Local "kitchen-sink" envs
+# (e.g. pangeo) hide missing deps; CI builds strictly from this file and will
+# silently produce empty notebook cells if anything is missing.
+#
+# pixi.lock (committed alongside this file) pins every package to an exact
+# build hash per platform. Regenerate it with `pixi install` after editing
+# this file; commit both files in the same commit.
+
+[workspace]
+name = "{{REPO_NAME}}"
+# bioconda hosts snakemake (and downstream rule-engine ecosystem); conda-forge
+# is the priority channel for everything else.
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64", "osx-arm64", "win-64"]
+
+[dependencies]
+python = "3.12.*"
+# --- core scientific stack ---
+numpy = "*"
+pandas = ">=2.0"
+xarray = ">=2024.6"
+scipy = "*"
+matplotlib = "*"
+pyarrow = "*"
+# --- notebook execution + Jupyter Book ---
+jupytext = "*"
+jupyterlab = "*"
+nbclient = "*"
+ipykernel = "*"
+# --- pipeline driver ---
+snakemake = "*"
+# --- replace/extend with the deps your replication needs ---
+# Examples (uncomment as needed):
+# statsmodels = "*"          # GLM/GLMM regression
+# scikit-learn = "*"         # classical ML
+# pyproj = "*"               # CRS + map projections
+# cartopy = "*"              # geographic plotting
+# netcdf4 = "*"              # NetCDF I/O — preferred over .npz for arrays (see DOMAIN.md)
+# zarr = "*"                 # Zarr — preferred for arrays >2 GB or cloud-archived (see DOMAIN.md)
+# cdsapi = "*"               # Copernicus Climate Data Store
+# copernicusmarine = "*"     # Copernicus Marine Service
+# healpix-geo = "*"          # HEALPix on geo data — preferred (use nest=True — see DOMAIN.md)
+# healpy = "*"               # HEALPix on pure-sphere (astrophysics) only
+# rasterio = "*"             # raster I/O
+# geopandas = "*"            # vector I/O
+# dask = "*"                 # out-of-core / parallel
+
+# Pip-only deps go in [pypi-dependencies]. Conda-forge is preferred where available.
+# [pypi-dependencies]
+# pygbif = "*"               # GBIF occurrences
+# polytope-client = "*"      # Destination Earth Climate DT
+# earthkit-data = "*"
+
+[feature.docs.dependencies]
+mystmd = "*"
+
+[feature.tests.dependencies]
+pytest = "*"
+
+[environments]
+default = { solve-group = "default" }
+docs = { features = ["docs"], solve-group = "default" }
+tests = { features = ["tests"], solve-group = "default" }
+
+[tasks]
+run = "snakemake --cores 1"
+book = "myst build --html"
+lab = "jupyter lab"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 16eed3b..041e32c 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,8 @@
       "mainEntity": { "@id": "Snakefile" },
       "hasPart": [
         { "@id": "Snakefile" },
-        { "@id": "environment.yml" },
+        { "@id": "pixi.toml" },
+        { "@id": "pixi.lock" },
         { "@id": "Dockerfile" },
         { "@id": "notebooks/01_data_download.py" },
         { "@id": "notebooks/02_data_clean.py" },
@@ -51,7 +52,7 @@
       "name": "Replication pipeline",
       "description": "Snakemake workflow orchestrating data download, cleaning, analysis, and figure generation.",
       "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#snakemake" },
-      "input": [{ "@id": "paper/" }, { "@id": "environment.yml" }],
+      "input": [{ "@id": "paper/" }, { "@id": "pixi.toml" }, { "@id": "pixi.lock" }],
       "output": [{ "@id": "results/" }, { "@id": "figures/" }, { "@id": "nanopubs/PUBLISHED.md" }]
     },
     {
@@ -61,9 +62,15 @@
       "url": "https://snakemake.readthedocs.io/"
     },
     {
-      "@id": "environment.yml",
+      "@id": "pixi.toml",
       "@type": ["File", "ConfigurationFile"],
-      "name": "Conda environment specification",
+      "name": "Pixi workspace manifest (declared dependencies, features, tasks)",
+      "encodingFormat": "application/toml"
+    },
+    {
+      "@id": "pixi.lock",
+      "@type": ["File", "ConfigurationFile"],
+      "name": "Pixi per-platform lockfile (every package pinned to an exact build hash)",
       "encodingFormat": "application/yaml"
     },
     {
diff --git a/scripts/import-nanopub-chain.py b/scripts/import-nanopub-chain.py
index abe3527..c62dccb 100644
--- a/scripts/import-nanopub-chain.py
+++ b/scripts/import-nanopub-chain.py
@@ -94,7 +94,8 @@
 # merges what they want into the new repo. Add to this list iteratively
 # as patterns emerge.
 SIBLING_INHERITED_FILES = [
-    "environment.yml",
+    "pixi.toml",
+    "pixi.lock",
     "Snakefile",
     "notebooks/01_data_download.py",
     "notebooks/02_data_clean.py",
@@ -620,10 +621,11 @@ def write_setup_inherited(out_path: Path,
     lines.extend([
         "## Suggested next steps",
         "",
-        "1. Open `_template_from_prior/environment.yml` and merge its pinned",
-        "   dependency versions into your own `environment.yml` (the staging",
-        "   file inherits Soroye-2020-era pins; add domain packages for your",
-        "   replication).",
+        "1. Open `_template_from_prior/pixi.toml` and merge its declared",
+        "   dependencies into your own `pixi.toml`; the matching",
+        "   `_template_from_prior/pixi.lock` carries the prior chain's",
+        "   per-platform pinned versions. After merging, run `pixi install`",
+        "   to refresh your own `pixi.lock`, then commit both files.",
         "2. Open `_template_from_prior/notebooks/01_data_download.py` to see",
         "   how the prior chain fetched climate / occurrence / paper data.",
         "   The patterns there — GBIF pre-minted-download style, Polytope",