From b2b74d99fd17dbf076c7423333761bdfdec4ae34 Mon Sep 17 00:00:00 2001
From: Luiz Irber <contact+github@luizirber.org>
Date: Tue, 13 Feb 2024 21:40:46 -0800
Subject: [PATCH] deploy docs scaffold

---
 docs/conf.py          |   3 +-
 docs/deploy.md        |  74 +++++++++++++++++
 docs/index.md         |   2 +
 docs/requirements.txt |   1 +
 flake.nix             |   1 +
 pixi.lock             | 182 ++++++++++++++++++++++++++++--------------
 pixi.toml             |  15 +++-
 tox.ini               |  21 +++++
 8 files changed, 235 insertions(+), 64 deletions(-)
 create mode 100644 docs/deploy.md
 create mode 100644 tox.ini

diff --git a/docs/conf.py b/docs/conf.py
index 25b7ec4..511fb84 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -25,7 +25,8 @@
     "myst_parser",
     "sphinx_copybutton",
     "sphinx_design",
-    "sphinx_inline_tabs"
+    "sphinx_inline_tabs",
+    "sphinxcontrib.mermaid"
 ]
 
 templates_path = ['_templates']
diff --git a/docs/deploy.md b/docs/deploy.md
new file mode 100644
index 0000000..fad0df8
--- /dev/null
+++ b/docs/deploy.md
@@ -0,0 +1,74 @@
+# Deploying a new branchwater instance
+
+Deploying a new `branchwater` instance involves bringing up a couple of components:
+- `branchwater-web`, the web frontend at [https://branchwater.sourmash.bio](https://branchwater.sourmash.bio)
+- `branchwater-server`, the backend serving the RocksDB inverted index for sourmash signatures
+- a [mongo](https://www.mongodb.com/) database for the SRA metadata used for
+  `branchwater-web` results
+
+A diagram of how these components are connected:
+
+::: {mermaid}
+graph LR;
+classDef server fill:#4A902A,stroke:#333,stroke-width:4px,color:#fff;
+classDef web fill:#dc6c11,stroke:#333,stroke-width:4px,color:#fff;
+classDef index fill:#3c48cc,stroke:#333,stroke-width:4px,color:#fff;
+classDef mongodb fill:#6980e9,stroke:#333,stroke-width:4px,color:#fff;
+classDef client fill:#8450e1,stroke:#333,stroke-width:4px,color:#fff;
+
+A01(browser):::client --> B01(web):::web
+B01 --> C01(server):::server
+B01 --> D01[(mongo)]:::mongodb
+C01 --> E01[(index)]:::index
+:::
+
+Be it for development or production usage,
+a [`docker-compose`](https://docs.docker.com/compose/)
+configuration is [available in the repo](https://github.com/sourmash-bio/branchwater/blob/main/docker-compose.yml)
+that can bring up these components in the appropriate order.
+
+## Bringing up branchwater with demo dataset
+
+### Clone the repo
+
+```
+git clone https://github.com/sourmash-bio/branchwater
+```
+
+### Set up dependencies
+
+```
+pixi shell
+
+```
+
+### The demo dataset
+
+```
+cat buildmongo/sra.runinfo.csv
+```
+(will probably move this into `experiments/` instead?)
+
+### Download signatures and prepare search index
+
+```
+pixi run index
+```
+
+### Bring up mongo for data loading
+
+```
+podman-compose up -d mongodb
+```
+
+### Download the SRA metadata from bigquery and load into mongo
+
+```
+pixi run metadata
+```
+
+### Bring up search index and web frontend
+
+```
+podman-compose up -d
+```
diff --git a/docs/index.md b/docs/index.md
index 5a9923b..e4d28f5 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -11,6 +11,8 @@ hide-toc: true
 
 ```{toctree}
 :hidden:
+
+deploy
 ```
 
 ```{toctree}
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 60bc06c..4537a85 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -4,3 +4,4 @@ sphinx-copybutton
 sphinx-design
 sphinx-inline-tabs
 sphinx-tabs
+sphinxcontrib-mermaid
diff --git a/flake.nix b/flake.nix
index 99293f0..a1f0248 100644
--- a/flake.nix
+++ b/flake.nix
@@ -190,6 +190,7 @@
               sphinx-design
               sphinx-inline-tabs
               sphinx-tabs
+              tox
             ]))
           ] ++ lib.optionals stdenv.isDarwin [
             darwin.apple_sdk.frameworks.Security
diff --git a/pixi.lock b/pixi.lock
index 72aba81..0b3aace 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5,17 +5,49 @@ environments:
     - url: https://conda.anaconda.org/conda-forge/
     - url: https://conda.anaconda.org/bioconda/
     packages: {}
-  snakemake:
+  deploy:
     channels:
     - url: https://conda.anaconda.org/conda-forge/
     - url: https://conda.anaconda.org/bioconda/
     packages:
       linux-64:
-      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-8.4.3-hdfd78af_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.1-h2797004_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.1-hab00c5b_1_cpython.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py312h98912ed_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/podman-compose-1.0.6-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.0.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda
+  prepare:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://conda.anaconda.org/bioconda/
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-8.4.8-hdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.15.3-pyhdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-8.2.0-pyhdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-3.0.0-pyhdfd78af_0.tar.bz2
-      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-8.4.3-pyhdfd78af_0.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-8.4.8-pyhdfd78af_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h30efb56_1.conda
@@ -43,14 +75,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapacke-3.9.0-21_linux64_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.26-pthreads_h413a1c8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.44.2-h2797004_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.1-h2797004_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.5-py312h98912ed_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.3-py312heda63a1_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py312heda63a1_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.0-py312hfb8ada1_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.8-py312h98912ed_0.conda
@@ -69,7 +101,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/argparse-dataclass-2.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/attmap-0.13.2-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2023.11.17-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/coincbc-2.10.10-0_metapackage.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
@@ -104,7 +136,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytest-8.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.19.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2023.4-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/referencing-0.33.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda
@@ -112,8 +144,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.7.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-69.0.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/slack-sdk-3.26.2-pyha770c72_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/slack_sdk-3.26.2-hd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/slack-sdk-3.27.0-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/slack_sdk-3.27.0-hd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/smart_open-6.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/smmap-5.0.0-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/stopit-1.1.2-py_0.tar.bz2
@@ -284,18 +316,18 @@ packages:
   timestamp: 1706843687645
 - kind: conda
   name: certifi
-  version: 2023.11.17
+  version: 2024.2.2
   build: pyhd8ed1ab_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/certifi-2023.11.17-pyhd8ed1ab_0.conda
-  sha256: afa22b77128a812cb57bc707c297d926561bd225a3d9dd74205d87a3b2d14a96
-  md5: 2011bcf45376341dd1d690263fdbc789
+  url: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda
+  sha256: f1faca020f988696e6b6ee47c82524c7806380b37cfdd1def32f92c326caca54
+  md5: 0876280e409658fc6f9e75d035960333
   depends:
   - python >=3.7
   license: ISC
-  size: 158939
-  timestamp: 1700303562512
+  size: 160559
+  timestamp: 1707022289175
 - kind: conda
   name: charset-normalizer
   version: 3.3.2
@@ -1001,18 +1033,18 @@ packages:
   timestamp: 1704950143521
 - kind: conda
   name: libsqlite
-  version: 3.44.2
+  version: 3.45.1
   build: h2797004_0
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.44.2-h2797004_0.conda
-  sha256: ee2c4d724a3ed60d5b458864d66122fb84c6ce1df62f735f90d8db17b66cd88a
-  md5: 3b6a9f225c3dbe0d24f4fedd4625c5bf
+  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.1-h2797004_0.conda
+  sha256: 1b379d1c652b25d0540251d422ef767472e768fd36b77261045e97f9ba6d3faa
+  md5: fc4ccadfbf6d4784de88c41704792562
   depends:
   - libgcc-ng >=12
   - libzlib >=1.2.13,<1.3.0a0
   license: Unlicense
-  size: 845830
-  timestamp: 1700863204572
+  size: 859346
+  timestamp: 1707495156652
 - kind: conda
   name: libstdcxx-ng
   version: 13.2.0
@@ -1170,12 +1202,12 @@ packages:
   timestamp: 1698751260967
 - kind: conda
   name: numpy
-  version: 1.26.3
+  version: 1.26.4
   build: py312heda63a1_0
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.3-py312heda63a1_0.conda
-  sha256: 6390aadc421c1059f8361d11e9127eb5b6ea38bda74d27abc696536f4bbb12b0
-  md5: 8b63634568b70ed9110f4d03dca20988
+  url: https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py312heda63a1_0.conda
+  sha256: fe3459c75cf84dcef6ef14efcc4adb0ade66038ddd27cadb894f34f4797687d8
+  md5: d8285bea2a350f63fab23bf460221f3f
   depends:
   - libblas >=3.9.0,<4.0a0
   - libcblas >=3.9.0,<4.0a0
@@ -1188,8 +1220,8 @@ packages:
   - numpy-base <0a0
   license: BSD-3-Clause
   license_family: BSD
-  size: 7491807
-  timestamp: 1704280741972
+  size: 7484186
+  timestamp: 1707225809722
 - kind: conda
   name: openssl
   version: 3.2.1
@@ -1324,6 +1356,23 @@ packages:
   license_family: MIT
   size: 23384
   timestamp: 1706116931972
+- kind: conda
+  name: podman-compose
+  version: 1.0.6
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/podman-compose-1.0.6-pyhd8ed1ab_0.conda
+  sha256: 43315af2ca8f11387f6d8d4da426f24b10253586cd77765124cf47110f0b95a1
+  md5: b670e2d683a55794e791633f68ede856
+  depends:
+  - python >=3.5
+  - python-dotenv
+  - pyyaml
+  license: GPL-2.0-only
+  license_family: GPL
+  size: 43937
+  timestamp: 1681059468664
 - kind: conda
   name: psutil
   version: 5.9.8
@@ -1474,6 +1523,21 @@ packages:
   license_family: APACHE
   size: 245987
   timestamp: 1626286448716
+- kind: conda
+  name: python-dotenv
+  version: 1.0.1
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.0.1-pyhd8ed1ab_0.conda
+  sha256: 2d4c80364f03315d606a50eddd493dbacc078e21412c2462c0f781eec49b572c
+  md5: c2997ea9360ac4e015658804a7a84f94
+  depends:
+  - python >=3.8
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 24278
+  timestamp: 1706018281544
 - kind: conda
   name: python-fastjsonschema
   version: 2.19.1
@@ -1491,19 +1555,19 @@ packages:
   timestamp: 1703781171097
 - kind: conda
   name: python-tzdata
-  version: '2023.4'
+  version: '2024.1'
   build: pyhd8ed1ab_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2023.4-pyhd8ed1ab_0.conda
-  sha256: d2381037bf362c78654a8ece0e0f54715e09113448ddd7ed837f688536cbf176
-  md5: c79cacf8a06a51552fc651652f170208
+  url: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.1-pyhd8ed1ab_0.conda
+  sha256: 9da9a849d53705dee450b83507df1ca8ffea5f83bd21a215202221f1c492f8ad
+  md5: 98206ea9954216ee7540f0c773f2104d
   depends:
   - python >=3.6
   license: Apache-2.0
   license_family: APACHE
-  size: 146007
-  timestamp: 1703878849208
+  size: 144024
+  timestamp: 1707747742930
 - kind: conda
   name: python_abi
   version: '3.12'
@@ -1687,34 +1751,34 @@ packages:
   timestamp: 1620240338595
 - kind: conda
   name: slack-sdk
-  version: 3.26.2
+  version: 3.27.0
   build: pyha770c72_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/slack-sdk-3.26.2-pyha770c72_0.conda
-  sha256: 8d7a9659e4d9912db590cb6d6ae7c6ebd5e72db0539329beca0e93a4d1b63562
-  md5: 92e17f98cf7d1eb53cef3e5260cbab89
+  url: https://conda.anaconda.org/conda-forge/noarch/slack-sdk-3.27.0-pyha770c72_0.conda
+  sha256: d55f004f21ddc3ffd7830c8170732a0e938f8e0e67f0cfb723901650a3a8beef
+  md5: 72a30cb842d392cd5169b8b952e962f6
   depends:
   - python >=3.6
   license: MIT
   license_family: MIT
-  size: 144399
-  timestamp: 1704787366538
+  size: 145842
+  timestamp: 1707808462213
 - kind: conda
   name: slack_sdk
-  version: 3.26.2
+  version: 3.27.0
   build: hd8ed1ab_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/slack_sdk-3.26.2-hd8ed1ab_0.conda
-  sha256: ca1f575dc1239eac5e43b6e8f19485d58827a46bbfda1f3ba3e2de1cea736f23
-  md5: 3eff2de31b65488b59faf5fc5b020c24
+  url: https://conda.anaconda.org/conda-forge/noarch/slack_sdk-3.27.0-hd8ed1ab_0.conda
+  sha256: 6cc2c7de14e94ce5df8d26e35d22079df4f14c5273c1dbcc77006858f434867a
+  md5: e809bc71c98d1ebddd018dee3c0a61c7
   depends:
-  - slack-sdk 3.26.2 pyha770c72_0
+  - slack-sdk 3.27.0 pyha770c72_0
   license: MIT
   license_family: MIT
-  size: 6428
-  timestamp: 1704787376372
+  size: 6375
+  timestamp: 1707808472526
 - kind: conda
   name: smart_open
   version: 6.4.0
@@ -1747,23 +1811,23 @@ packages:
   timestamp: 1634310465482
 - kind: conda
   name: snakemake
-  version: 8.4.3
+  version: 8.4.8
   build: hdfd78af_0
   subdir: noarch
   noarch: generic
-  url: https://conda.anaconda.org/bioconda/noarch/snakemake-8.4.3-hdfd78af_0.tar.bz2
-  sha256: 10673ea4587f175294bb9a56cbd2152e4f8cebe9f8dcfd672d0fde5f09943b06
-  md5: 1b9ffa8e999583d9d85a0afdee9338ea
+  url: https://conda.anaconda.org/bioconda/noarch/snakemake-8.4.8-hdfd78af_0.tar.bz2
+  sha256: b8871807298e71f3e98f662c13c78283abf877dd46e9916722c18043d1107c78
+  md5: 833308b3e7e943eb12ff956373e15cc3
   depends:
   - eido
   - pandas
   - peppy
   - pygments
   - slack_sdk
-  - snakemake-minimal 8.4.3.*
+  - snakemake-minimal 8.4.8.*
   license: MIT
-  size: 8780
-  timestamp: 1706873388154
+  size: 8792
+  timestamp: 1707499493195
 - kind: conda
   name: snakemake-interface-common
   version: 1.15.3
@@ -1819,13 +1883,13 @@ packages:
   timestamp: 1702992209726
 - kind: conda
   name: snakemake-minimal
-  version: 8.4.3
+  version: 8.4.8
   build: pyhdfd78af_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-8.4.3-pyhdfd78af_0.tar.bz2
-  sha256: edc55cd5712d6c251a3fe0e18876b4fbc89bff543ce7a86c7b25fe52d40bac58
-  md5: 721c6163ed5f3f6a139456570f346bf3
+  url: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-8.4.8-pyhdfd78af_0.tar.bz2
+  sha256: f75a50c3651ad0636cba6cf80ee9a16832cce07f4149f7cd0aab25467c809ca6
+  md5: b7174e4f0a1eed5f3379356e9f6a69d3
   depends:
   - appdirs
   - conda-inject >=1.3.1,<2.0
@@ -1858,8 +1922,8 @@ packages:
   - wrapt
   - yte >=1.5.1,<2.0
   license: MIT
-  size: 210904
-  timestamp: 1706873376343
+  size: 214427
+  timestamp: 1707499481467
 - kind: conda
   name: stopit
   version: 1.1.2
diff --git a/pixi.toml b/pixi.toml
index c734739..d863f04 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -3,13 +3,20 @@ name = "branchwater"
 channels = ["conda-forge", "bioconda"]
 platforms = ["linux-64"]
 
+[environments]
+prepare = ["prepare"]
+deploy = ["deploy"]
+
 [dependencies]
 
 [feature.prepare.tasks]
-snakemake = { cmd = ["snakemake"] }
+index = { cmd = ["snakemake"] }
+metadata = { cmd = ["podman-compose",
+                    "exec", "mongo",
+                    "python3", "/docker-entrypoint-initdb.d/bqtomongo.py"] }
 
 [feature.prepare.dependencies]
-snakemake = "*"
+snakemake = ">=8,<9"
 
-[environments]
-snakemake = ["prepare"]
+[feature.deploy.dependencies]
+podman-compose = "*"
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 0000000..c339563
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,21 @@
+[tox]
+isolated_build = true
+skip_missing_interpreters = true
+env_list =
+    docs,
+min_version = 3.27
+
+[testenv:docs]
+description = invoke sphinx-build to build the HTML docs
+basepython = python3.11
+deps =
+  -r docs/requirements.txt
+commands =
+    sphinx-build -d "{toxworkdir}/docs_doctree" docs "{toxworkdir}/docs_out" --color -bhtml {posargs}
+    python -c 'import pathlib; print("documentation available under file://\{0\}".format(pathlib.Path(r"{toxworkdir}") / "docs_out" / "index.html"))'
+allowlist_externals = pandoc
+change_dir = {toxinidir}
+pass_env =
+    HOME
+    LC_ALL
+    LOCALE_*