From 41ad57027b3748890a546fd5faca5c599d05170b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 09:40:39 +0100
Subject: [PATCH 01/13] Bump pillow from 10.0.1 to 10.2.0 (#377)

Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.1 to 10.2.0.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](https://github.com/python-pillow/Pillow/compare/10.0.1...10.2.0)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock | 128 ++++++++++++++++++++++++++++++----------------------
 1 file changed, 73 insertions(+), 55 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9b5bc9f..47d8800 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1175,70 +1175,88 @@ files = [
 
 [[package]]
 name = "pillow"
-version = "10.0.1"
+version = "10.2.0"
 description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
 docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
+fpx = ["olefile"]
+mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+typing = ["typing-extensions"]
+xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"

From da83b6b7369349e84f5c6832fc64689bfc6f4fc6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 16:21:11 +0100
Subject: [PATCH 02/13] Bump pytest from 7.4.4 to 8.0.0 (#382)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.4 to 8.0.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.4.4...8.0.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 20 ++++++++++----------
 pyproject.toml |  2 +-
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 47d8800..df7783e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1290,13 +1290,13 @@ tenacity = ">=6.2.0"
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.4.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"},
-    {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"},
+    {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
+    {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
 ]
 
 [package.extras]
@@ -1340,13 +1340,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.4"
+version = "8.0.0"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
-    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
+    {file = "pytest-8.0.0-py3-none-any.whl", hash = "sha256:50fb9cbe836c3f20f0dfa99c565201fb75dc54c8d76373cd1bde06b06657bdb6"},
+    {file = "pytest-8.0.0.tar.gz", hash = "sha256:249b1b0864530ba251b7438274c4d251c58d868edaaec8762893ad4a0d71c36c"},
 ]
 
 [package.dependencies]
@@ -1354,7 +1354,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
+pluggy = ">=1.3.0,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
@@ -1589,4 +1589,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "d234f041acaa1b028c3c2a9aae1646d0c782e5091669252acfb6727d55f2e778"
+content-hash = "c01c14f5a8298310b9016dab762f61f30a311a251ac66f89f91dd00100add9f1"
diff --git a/pyproject.toml b/pyproject.toml
index dcb3c20..ebd1ec3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ arctic3d-localise = "arctic3d.cli_localise:maincli"
 arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4.4"
+pytest = "^8.0.0"
 pytest-cov = "^4.1.0"
 coverage = "^7.3.2"
 hypothesis = "^6.92.2"

From bc9108e197f0a0349ccfa936b777d1c6165c8d6e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 16:58:32 +0100
Subject: [PATCH 03/13] Bump biopython from 1.81 to 1.83 (#379)

Bumps [biopython](https://github.com/biopython/biopython) from 1.81 to 1.83.
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

---
updated-dependencies:
- dependency-name: biopython
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 56 ++++++++++++++++++++++----------------------------
 pyproject.toml |  2 +-
 2 files changed, 26 insertions(+), 32 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index df7783e..5fc3de7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -39,39 +39,33 @@ tqdm = "*"
 
 [[package]]
 name = "biopython"
-version = "1.81"
+version = "1.83"
 description = "Freely available tools for computational molecular biology."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1589,4 +1583,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "c01c14f5a8298310b9016dab762f61f30a311a251ac66f89f91dd00100add9f1"
+content-hash = "a4981b5e0b31b64c57de0484ebde6652755d1daa6751491175eb5f09abf10464"
diff --git a/pyproject.toml b/pyproject.toml
index ebd1ec3..e8046ed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,7 @@ defusedxml = "0.7.1"
 lxml = "5.0.0"
 mdanalysis = "2.7.0"
 requests = "2.31.0"
-biopython = "1.81"
+biopython = "1.83"
 scipy = "1.11.4"
 matplotlib = "3.8.2"
 pdb-tools = "2.5.0"

From 0b5dc37b789e22f8c10416b9d061463df992ef8d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 17:10:29 +0100
Subject: [PATCH 04/13] Bump bio from 1.6.0 to 1.6.2 (#383)

Bumps [bio](https://github.com/ialbert/bio) from 1.6.0 to 1.6.2.
- [Commits](https://github.com/ialbert/bio/commits)

---
updated-dependencies:
- dependency-name: bio
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 6 +++---
 pyproject.toml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5fc3de7..006202e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -20,12 +20,12 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy
 
 [[package]]
 name = "bio"
-version = "1.6.0"
+version = "1.6.2"
 description = "bio"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "bio-1.6.0-py3-none-any.whl", hash = "sha256:38b14e11625ef233e1a3878c8b13253695e863bd997f94715c248b71612605d5"},
+    {file = "bio-1.6.2-py3-none-any.whl", hash = "sha256:dcec8207f3993a7f41bd8205cde235218da3dc008175ae7bb7468276d8dacf71"},
 ]
 
 [package.dependencies]
@@ -1583,4 +1583,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "a4981b5e0b31b64c57de0484ebde6652755d1daa6751491175eb5f09abf10464"
+content-hash = "006cc583bad35fb24707c4a7ae607e5684cd4e3b4b07233487e5af3807b4e2e7"
diff --git a/pyproject.toml b/pyproject.toml
index e8046ed..c672ddb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bio = "1.6.0"
+bio = "1.6.2"
 defusedxml = "0.7.1"
 lxml = "5.0.0"
 mdanalysis = "2.7.0"

From fe10eb6fc18fd060f6c12c5e322d13b7d0e73b20 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 17:23:30 +0100
Subject: [PATCH 05/13] Bump coverage from 7.3.2 to 7.4.1 (#381)

Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.3.2 to 7.4.1.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](https://github.com/nedbat/coveragepy/compare/7.3.2...7.4.1)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 108 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   2 +-
 2 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 006202e..3de803d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -285,63 +285,63 @@ test-no-images = ["pytest"]
 
 [[package]]
 name = "coverage"
-version = "7.3.2"
+version = "7.4.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1583,4 +1583,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "006cc583bad35fb24707c4a7ae607e5684cd4e3b4b07233487e5af3807b4e2e7"
+content-hash = "818c16f83dc5cc9ce6ebe18c2396bb3986adc5c8c83b834887a6da7e181a86be"
diff --git a/pyproject.toml b/pyproject.toml
index c672ddb..32c2d6c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,7 @@ arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.0.0"
 pytest-cov = "^4.1.0"
-coverage = "^7.3.2"
+coverage = "^7.4.1"
 hypothesis = "^6.92.2"
 
 [tool.black]

From ea9d049f402e78a7d8450a31c191a33524a3af89 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 17:46:15 +0100
Subject: [PATCH 06/13] Bump lxml from 5.0.0 to 5.1.0 (#380)

Bumps [lxml](https://github.com/lxml/lxml) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-5.0.0...lxml-5.1.0)

---
updated-dependencies:
- dependency-name: lxml
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 172 +++++++++++++++++++++++--------------------------
 pyproject.toml |   2 +-
 2 files changed, 82 insertions(+), 92 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 3de803d..f51c7b9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -696,99 +696,89 @@ files = [
 
 [[package]]
 name = "lxml"
-version = "5.0.0"
+version = "5.1.0"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
+python-versions = ">=3.6"
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+    {file = "lxml-5.1.0.tar.gz", hash = "sha256:3eea6ed6e6c918e468e693c41ef07f3c3acc310b70ddd9cc72d9ef84bc9564ca"},
 ]
 
 [package.extras]
@@ -1583,4 +1573,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "818c16f83dc5cc9ce6ebe18c2396bb3986adc5c8c83b834887a6da7e181a86be"
+content-hash = "e7d38e43a44fa9a7165a57fb3b0ca3a92ce490b793a4549dfd7e538320d3ffd7"
diff --git a/pyproject.toml b/pyproject.toml
index 32c2d6c..804c85f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ classifiers = [
 python = ">=3.9,<3.12"
 bio = "1.6.2"
 defusedxml = "0.7.1"
-lxml = "5.0.0"
+lxml = "5.1.0"
 mdanalysis = "2.7.0"
 requests = "2.31.0"
 biopython = "1.83"

From 14f71e5e010d5ab3893a0c2b0d6e234e0dc709ef Mon Sep 17 00:00:00 2001
From: Marco Giulini <54807167+mgiulini@users.noreply.github.com>
Date: Tue, 6 Feb 2024 12:34:39 +0100
Subject: [PATCH 07/13] Prettier readmes (#385)

* Update README.md

* Update CONTRIBUTING.md

* added space
---
 CONTRIBUTING.md |  2 --
 README.md       | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 4d67ca2..156ec0f 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,7 +1,5 @@
 # Developing ARCTIC-3D
 
-This section is still work in progress
-
 ## Installation
 
 We use `poetry` to manage the dependencies and the virtual environment, so it makes things easier if you need to install it first; check the [official documentation](https://python-poetry.org/docs/#installation) for more details.
diff --git a/README.md b/README.md
index 437648f..f3c5138 100644
--- a/README.md
+++ b/README.md
@@ -28,6 +28,15 @@ Check [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 
 ### With `conda`
 
+Clone the repository on your computer and navigate to it
+
+```bash
+git clone git@github.com:haddocking/arctic3d.git
+cd arctic3d
+```
+
+Here you can create the arctic3d environment:
+
 ```bash
 conda create -n arctic3d python=3.10
 conda activate arctic3d
@@ -59,3 +68,9 @@ sphinx-build -E docs ./arctic3d-docs
 ```
 
 Then you can open the file `arctic3d-docs/index.html`, which contains all the necessary documentation.
+
+## Citing us
+
+If you used ARCTIC-3D in your work please cite the following publication:
+
+**Marco Giulini, Rodrigo V. Honorato, Jesús L. Rivera, and Alexandre MJJ Bonvin**: "ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information." Communications Biology 7, no. 1 (2024): 49. (www.nature.com/articles/s42003-023-05718-w)

From 213f727cce4f8768dd295553ba60196ae465561c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Mar 2024 16:45:57 +0100
Subject: [PATCH 08/13] Bump jsonpickle from 3.0.2 to 3.0.3 (#390)

Bumps [jsonpickle](https://github.com/jsonpickle/jsonpickle) from 3.0.2 to 3.0.3.
- [Changelog](https://github.com/jsonpickle/jsonpickle/blob/main/CHANGES.rst)
- [Commits](https://github.com/jsonpickle/jsonpickle/compare/v3.0.2...v3.0.3)

---
updated-dependencies:
- dependency-name: jsonpickle
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 18 +++++++++++-------
 pyproject.toml |  2 +-
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f51c7b9..efcc300 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -45,23 +45,28 @@ optional = false
 python-versions = ">=3.8"
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@@ -588,19 +593,18 @@ files = [
 
 [[package]]
 name = "jsonpickle"
-version = "3.0.2"
+version = "3.0.3"
 description = "Python library for serializing any arbitrary object graph into JSON"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
-docs = ["jaraco.packaging (>=3.2)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["ecdsa", "feedparser", "gmpy2", "numpy", "pandas", "pymongo", "pytest (>=3.5,!=3.7.3)", "pytest-black-multipy", "pytest-checkdocs (>=1.2.3)", "pytest-cov", "pytest-flake8 (>=1.1.1)", "scikit-learn", "sqlalchemy"]
-testing-libs = ["simplejson", "ujson"]
+docs = ["furo", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"]
+testing = ["ecdsa", "feedparser", "gmpy2", "numpy", "pandas", "pymongo", "pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-ruff", "scikit-learn", "simplejson", "sqlalchemy", "ujson"]
 
 [[package]]
 name = "kaleido"
@@ -1573,4 +1577,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "e7d38e43a44fa9a7165a57fb3b0ca3a92ce490b793a4549dfd7e538320d3ffd7"
+content-hash = "0c938ebea0615f3807ce47d0027c7bb4fed3d87acfdaa7f871437514f8626221"
diff --git a/pyproject.toml b/pyproject.toml
index 804c85f..6b8027b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ pandas = "2.1.4"
 openpyxl = "3.1.2"
 plotly = "5.18.0"
 pdbecif = "1.5"
-jsonpickle = "3.0.2"
+jsonpickle = "3.0.3"
 kaleido = "0.2.1"
 
 [tool.poetry.scripts]

From f9f0019d2d9ec580bfb127f02f25aa8a4a466cd8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Mar 2024 17:14:21 +0100
Subject: [PATCH 09/13] Bump coverage from 7.4.1 to 7.4.3 (#389)

Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.4.1 to 7.4.3.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](https://github.com/nedbat/coveragepy/compare/7.4.1...7.4.3)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 108 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   2 +-
 2 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index efcc300..38c61ca 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -290,63 +290,63 @@ test-no-images = ["pytest"]
 
 [[package]]
 name = "coverage"
-version = "7.4.1"
+version = "7.4.3"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
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+    {file = "coverage-7.4.3-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b9a4a8dd3dcf4cbd3165737358e4d7dfbd9d59902ad11e3b15eebb6393b0446e"},
+    {file = "coverage-7.4.3-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:062b0a75d9261e2f9c6d071753f7eef0fc9caf3a2c82d36d76667ba7b6470003"},
+    {file = "coverage-7.4.3-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:ebe7c9e67a2d15fa97b77ea6571ce5e1e1f6b0db71d1d5e96f8d2bf134303c1d"},
+    {file = "coverage-7.4.3-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:c0a120238dd71c68484f02562f6d446d736adcc6ca0993712289b102705a9a3a"},
+    {file = "coverage-7.4.3-cp312-cp312-win32.whl", hash = "sha256:37389611ba54fd6d278fde86eb2c013c8e50232e38f5c68235d09d0a3f8aa352"},
+    {file = "coverage-7.4.3-cp312-cp312-win_amd64.whl", hash = "sha256:d25b937a5d9ffa857d41be042b4238dd61db888533b53bc76dc082cb5a15e914"},
+    {file = "coverage-7.4.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:28ca2098939eabab044ad68850aac8f8db6bf0b29bc7f2887d05889b17346454"},
+    {file = "coverage-7.4.3-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:280459f0a03cecbe8800786cdc23067a8fc64c0bd51dc614008d9c36e1659d7e"},
+    {file = "coverage-7.4.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6c0cdedd3500e0511eac1517bf560149764b7d8e65cb800d8bf1c63ebf39edd2"},
+    {file = "coverage-7.4.3-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9a9babb9466fe1da12417a4aed923e90124a534736de6201794a3aea9d98484e"},
+    {file = "coverage-7.4.3-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dec9de46a33cf2dd87a5254af095a409ea3bf952d85ad339751e7de6d962cde6"},
+    {file = "coverage-7.4.3-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:16bae383a9cc5abab9bb05c10a3e5a52e0a788325dc9ba8499e821885928968c"},
+    {file = "coverage-7.4.3-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:2c854ce44e1ee31bda4e318af1dbcfc929026d12c5ed030095ad98197eeeaed0"},
+    {file = "coverage-7.4.3-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:ce8c50520f57ec57aa21a63ea4f325c7b657386b3f02ccaedeccf9ebe27686e1"},
+    {file = "coverage-7.4.3-cp38-cp38-win32.whl", hash = "sha256:708a3369dcf055c00ddeeaa2b20f0dd1ce664eeabde6623e516c5228b753654f"},
+    {file = "coverage-7.4.3-cp38-cp38-win_amd64.whl", hash = "sha256:1bf25fbca0c8d121a3e92a2a0555c7e5bc981aee5c3fdaf4bb7809f410f696b9"},
+    {file = "coverage-7.4.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3b253094dbe1b431d3a4ac2f053b6d7ede2664ac559705a704f621742e034f1f"},
+    {file = "coverage-7.4.3-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:77fbfc5720cceac9c200054b9fab50cb2a7d79660609200ab83f5db96162d20c"},
+    {file = "coverage-7.4.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6679060424faa9c11808598504c3ab472de4531c571ab2befa32f4971835788e"},
+    {file = "coverage-7.4.3-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4af154d617c875b52651dd8dd17a31270c495082f3d55f6128e7629658d63765"},
+    {file = "coverage-7.4.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8640f1fde5e1b8e3439fe482cdc2b0bb6c329f4bb161927c28d2e8879c6029ee"},
+    {file = "coverage-7.4.3-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:69b9f6f66c0af29642e73a520b6fed25ff9fd69a25975ebe6acb297234eda501"},
+    {file = "coverage-7.4.3-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:0842571634f39016a6c03e9d4aba502be652a6e4455fadb73cd3a3a49173e38f"},
+    {file = "coverage-7.4.3-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:a78ed23b08e8ab524551f52953a8a05d61c3a760781762aac49f8de6eede8c45"},
+    {file = "coverage-7.4.3-cp39-cp39-win32.whl", hash = "sha256:c0524de3ff096e15fcbfe8f056fdb4ea0bf497d584454f344d59fce069d3e6e9"},
+    {file = "coverage-7.4.3-cp39-cp39-win_amd64.whl", hash = "sha256:0209a6369ccce576b43bb227dc8322d8ef9e323d089c6f3f26a597b09cb4d2aa"},
+    {file = "coverage-7.4.3-pp38.pp39.pp310-none-any.whl", hash = "sha256:7cbde573904625509a3f37b6fecea974e363460b556a627c60dc2f47e2fffa51"},
+    {file = "coverage-7.4.3.tar.gz", hash = "sha256:276f6077a5c61447a48d133ed13e759c09e62aff0dc84274a68dc18660104d52"},
 ]
 
 [package.dependencies]
@@ -1577,4 +1577,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "0c938ebea0615f3807ce47d0027c7bb4fed3d87acfdaa7f871437514f8626221"
+content-hash = "14c884428d1bc63f103028cd8aa8f396097450159075ee028f80302320d59107"
diff --git a/pyproject.toml b/pyproject.toml
index 6b8027b..97683c9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,7 @@ arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.0.0"
 pytest-cov = "^4.1.0"
-coverage = "^7.4.1"
+coverage = "^7.4.3"
 hypothesis = "^6.92.2"
 
 [tool.black]

From 2c3079e458614126ed1af0b4d7e2cc702319b8bc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Mar 2024 09:58:35 +0100
Subject: [PATCH 10/13] Bump hypothesis from 6.92.2 to 6.98.15 (#386)

Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.92.2 to 6.98.15.
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.92.2...hypothesis-python-6.98.15)

---
updated-dependencies:
- dependency-name: hypothesis
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 12 ++++++------
 pyproject.toml |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 38c61ca..04fb457 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -510,13 +510,13 @@ scipy = "*"
 
 [[package]]
 name = "hypothesis"
-version = "6.92.2"
+version = "6.98.15"
 description = "A library for property-based testing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "hypothesis-6.92.2-py3-none-any.whl", hash = "sha256:d335044492acb03fa1fdb4edacb81cca2e578049fc7306345bc0e8947fef15a9"},
-    {file = "hypothesis-6.92.2.tar.gz", hash = "sha256:841f89a486c43bdab55698de8929bd2635639ec20bf6ce98ccd75622d7ee6d41"},
+    {file = "hypothesis-6.98.15-py3-none-any.whl", hash = "sha256:5b40fd81fce9e0b35f0a47e10eb41f375a6b9e8551d0e1084c83b8b0d0d1bb6b"},
+    {file = "hypothesis-6.98.15.tar.gz", hash = "sha256:1e31210951511b24ce8b3b6e04d791c466385a30ac3af571bf2223954b025d77"},
 ]
 
 [package.dependencies]
@@ -525,7 +525,7 @@ exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 sortedcontainers = ">=2.1.0,<3.0.0"
 
 [package.extras]
-all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "django (>=3.2)", "dpcontracts (>=0.4)", "lark (>=0.10.1)", "libcst (>=0.3.16)", "numpy (>=1.17.3)", "pandas (>=1.1)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2023.3)"]
+all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "django (>=3.2)", "dpcontracts (>=0.4)", "lark (>=0.10.1)", "libcst (>=0.3.16)", "numpy (>=1.17.3)", "pandas (>=1.1)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2024.1)"]
 cli = ["black (>=19.10b0)", "click (>=7.0)", "rich (>=9.0.0)"]
 codemods = ["libcst (>=0.3.16)"]
 dateutil = ["python-dateutil (>=1.4)"]
@@ -538,7 +538,7 @@ pandas = ["pandas (>=1.1)"]
 pytest = ["pytest (>=4.6)"]
 pytz = ["pytz (>=2014.1)"]
 redis = ["redis (>=3.0.0)"]
-zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2023.3)"]
+zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2024.1)"]
 
 [[package]]
 name = "idna"
@@ -1577,4 +1577,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "14c884428d1bc63f103028cd8aa8f396097450159075ee028f80302320d59107"
+content-hash = "1519c81479d18e8dc25d05cc0805ce6f61b020b2b5e24ad7fa2de2ee352d1e45"
diff --git a/pyproject.toml b/pyproject.toml
index 97683c9..42e0c7f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 pytest = "^8.0.0"
 pytest-cov = "^4.1.0"
 coverage = "^7.4.3"
-hypothesis = "^6.92.2"
+hypothesis = "^6.98.15"
 
 [tool.black]
 line-length = 79

From 17b17135e133ff44f5752250cd86848dde4badfd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Mar 2024 10:02:59 +0100
Subject: [PATCH 11/13] Bump plotly from 5.18.0 to 5.19.0 (#388)

Bumps [plotly](https://github.com/plotly/plotly.py) from 5.18.0 to 5.19.0.
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md)
- [Commits](https://github.com/plotly/plotly.py/compare/v5.18.0...v5.19.0)

---
updated-dependencies:
- dependency-name: plotly
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 10 +++++-----
 pyproject.toml |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 04fb457..309cbc0 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1263,13 +1263,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytes
 
 [[package]]
 name = "plotly"
-version = "5.18.0"
+version = "5.19.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "plotly-5.18.0-py3-none-any.whl", hash = "sha256:23aa8ea2f4fb364a20d34ad38235524bd9d691bf5299e800bca608c31e8db8de"},
-    {file = "plotly-5.18.0.tar.gz", hash = "sha256:360a31e6fbb49d12b007036eb6929521343d6bee2236f8459915821baefa2cbb"},
+    {file = "plotly-5.19.0-py3-none-any.whl", hash = "sha256:906abcc5f15945765328c5d47edaa884bc99f5985fbc61e8cd4dc361f4ff8f5a"},
+    {file = "plotly-5.19.0.tar.gz", hash = "sha256:5ea91a56571292ade3e3bc9bf712eba0b95a1fb0a941375d978cc79432e055f4"},
 ]
 
 [package.dependencies]
@@ -1577,4 +1577,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "1519c81479d18e8dc25d05cc0805ce6f61b020b2b5e24ad7fa2de2ee352d1e45"
+content-hash = "b166cc9f389279961e7aeb6d932ff58c386ecbe972b87fa901e1bf18269256e6"
diff --git a/pyproject.toml b/pyproject.toml
index 42e0c7f..280be61 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ matplotlib = "3.8.2"
 pdb-tools = "2.5.0"
 pandas = "2.1.4"
 openpyxl = "3.1.2"
-plotly = "5.18.0"
+plotly = "5.19.0"
 pdbecif = "1.5"
 jsonpickle = "3.0.3"
 kaleido = "0.2.1"

From ff9c43026f3fc63b552d89584078ea0ae13c5137 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Mar 2024 10:38:32 +0100
Subject: [PATCH 12/13] Bump pytest from 8.0.0 to 8.1.0 (#391)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.0.0 to 8.1.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.0.0...8.1.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock    | 14 +++++++-------
 pyproject.toml |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 309cbc0..dd6f9da 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1328,13 +1328,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "8.0.0"
+version = "8.1.0"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pytest-8.0.0-py3-none-any.whl", hash = "sha256:50fb9cbe836c3f20f0dfa99c565201fb75dc54c8d76373cd1bde06b06657bdb6"},
-    {file = "pytest-8.0.0.tar.gz", hash = "sha256:249b1b0864530ba251b7438274c4d251c58d868edaaec8762893ad4a0d71c36c"},
+    {file = "pytest-8.1.0-py3-none-any.whl", hash = "sha256:ee32db7af8de4629a455806befa90559f307424c07b8413ccfc30bf5b221dd7e"},
+    {file = "pytest-8.1.0.tar.gz", hash = "sha256:f8fa04ab8f98d185113ae60ea6d79c22f8143b14bc1caeced44a0ab844928323"},
 ]
 
 [package.dependencies]
@@ -1342,11 +1342,11 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=1.3.0,<2.0"
-tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
+pluggy = ">=1.4,<2.0"
+tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
@@ -1577,4 +1577,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "b166cc9f389279961e7aeb6d932ff58c386ecbe972b87fa901e1bf18269256e6"
+content-hash = "6a1cb7689a7a3a39b21aa8a238c555404f231e72e82a3d6c6b51a36637621a22"
diff --git a/pyproject.toml b/pyproject.toml
index 280be61..d64cfbe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ arctic3d-localise = "arctic3d.cli_localise:maincli"
 arctic3d-restraints = "arctic3d.cli_restraints:maincli"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^8.0.0"
+pytest = "^8.1.0"
 pytest-cov = "^4.1.0"
 coverage = "^7.4.3"
 hypothesis = "^6.98.15"

From 6dea3eadf6361d3c69d67b42189d8582543cccd7 Mon Sep 17 00:00:00 2001
From: Rodrigo Vargas Honorato <rvhonorato@gmail.com>
Date: Tue, 19 Mar 2024 16:11:08 +0100
Subject: [PATCH 13/13] Add Dockerfile and GitHub Actions workflow for building
 and publishing Docker image (#392)

---
 .github/workflows/docker-publish.yml | 47 ++++++++++++++++++++++++++++
 Dockerfile                           |  6 ++++
 2 files changed, 53 insertions(+)
 create mode 100644 .github/workflows/docker-publish.yml
 create mode 100644 Dockerfile

diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
new file mode 100644
index 0000000..9768afb
--- /dev/null
+++ b/.github/workflows/docker-publish.yml
@@ -0,0 +1,47 @@
+name: build and publish image
+
+on:
+  push:
+    # run only against tags
+    tags:
+      - "*"
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..5c1c206
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,6 @@
+FROM python:3.10
+WORKDIR /opt/software
+COPY . .
+RUN pip install .
+WORKDIR /data
+ENTRYPOINT [ "arctic3d" ]