Merge pull request #115 from cokelaer/main

Update to be poetry2 compatible.

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.8, 3.9,'3.10', '3.11']
+        python: [3.9,'3.10', '3.11']
       fail-fast: false
 
 
@@ -43,8 +43,7 @@ jobs:
     - name: install package itself
       run: |
          pip install poetry
-         pip install kaleido #required on github CI by plotly
-         poetry install
+         poetry install --with dev
 
     - name: testing
       run: |

README.rst

@@ -16,18 +16,23 @@
 .. image:: https://app.codacy.com/project/badge/Grade/9031e4e4213e4e57a876fd5b792b5003
    :target: https://app.codacy.com/gh/sequana/sequana_pipetools/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
 
+.. image:: https://img.shields.io/badge/python-3.9%20|%203.10%20|%203.11-blue
+    :target: https://www.python.org/
+    :alt: Python versions
+
 .. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
    :target: http://joss.theoj.org/papers/10.21105/joss.00352
    :alt: JOSS (journal of open source software) DOI
 
+
+
 :Overview: A set of tools to help building or using Sequana pipelines
 :Status: Production
 :Issues: Please fill a report on `github <https://github.com/sequana/sequana_pipetools/issues>`__
-:Python version: Python 3.8, 3.9, 3.10, 3.11
 :Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352,  `JOSS DOI doi:10.21105/joss.00352 <http://www.doi2bib.org/bib/10.21105%2Fjoss.00352>`_
 
-Installation
-============
+🔧 Installation
+===============
 
 from pypi website::
 
@@ -312,6 +317,8 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+1.2.0     * update to be compatible with poetry 2.0
+          * print container size when initiating a pipeline
 1.1.1     * symlink creation on apptainers skipped if permission error (file
             is probably already present and created by another users e.g.
             the admin system)
@@ -427,3 +434,8 @@ Version   Description
             from sequana.pipeline_common
 0.1.X     * software creation
 ========= ======================================================================
+
+
+## 🗨️ Contacts <a name="contacts"></a>
+
+For questions, feel free to reach out to the maintainers through GitHub.

pyproject.toml

@@ -1,14 +1,13 @@
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core>=2.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 
-#maintainer ?#maintainer email
-[tool.poetry]
+[project]
 name = "sequana_pipetools"
-version = "1.1.1"
+version = "1.2.0"
 description = "A set of tools to help building or using Sequana pipelines"
-authors = ["Sequana Team"]
+authors = [{name="Sequana Team", email="thomas.cokelaer@pasteur.fr"}]
 license = "BSD-3"
 repository = "https://github.com/sequana/sequana_pipetools"
 readme = "README.rst"
@@ -21,7 +20,6 @@ classifiers = [
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: BSD License",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
@@ -33,28 +31,28 @@ classifiers = [
 packages = [
     { include = "sequana_pipetools" }
 ]
+requires-python = ">=3.8,<4.0"
+dependencies = [
+    "easydev >=0.12",
+    "parse >=1.19.0",
+    "ruamel.yaml >=0.18.5",
+    "packaging  >=23.1",
+    "pykwalify >=1.8",
+    "importlib_resources >=5.4.0",
+    "pyyaml >=1.3",
+    "aiohttp >=3.8.4",
+    "tqdm >=4.65",
+    "charset-normalizer >=2",
+    "rich-click >=1.7.1",
+    "cookiecutter >=2.6.0",
+    "docutils (>0.20,!=0.21)",
+    "versionix (>=0.99.2,<0.100.0)"
+]
 
-[tool.poetry.dependencies]
-python = ">=3.8,<4.0"
-easydev = ">=0.12"
-parse = ">=1.19.0"
-"ruamel.yaml" = ">=0.18.5"
-packaging = ">=23.1"
-pykwalify = ">=1.8"
-importlib_resources = ">=5.4.0"
-pyyaml = ">=1.3"
-aiohttp = ">=3.8.4"
-tqdm = ">=4.65"
-charset-normalizer = ">=2"
-versionix = ">=0.2.0"
-rich-click = "^1.7.1"
-docutils = "^0.20"
-cookiecutter = "^2.6.0"
 
-[tool.poetry.scripts]
+[project.scripts]
 sequana_pipetools = "sequana_pipetools.scripts.main:main"
 
-
 [tool.poetry.group.dev.dependencies]
 black = "^23.7.0"
 pytest = "^8.0.0"

sequana_pipetools/misc.py

@@ -124,6 +124,19 @@ def levenshtein_distance(token1: str, token2: str) -> int:
     return distances[len1][len2]
 
 
+def get_url_file_size(url):
+    try:
+        response = requests.head(url, allow_redirects=True)
+        if response.status_code == 200 and "Content-Length" in response.headers:
+            return int(response.headers["Content-Length"])
+        else:
+            logger.warning(f"Unable to retrieve file size from {url}. Status code:", response.status_code)
+            return 0
+    except requests.RequestException as e:
+        logger.warning(f"Unable to retrieve file size from {url}:", e)
+        return 0
+
+
 def url2hash(url):
     md5hash = hashlib.md5()
     md5hash.update(url.encode())

sequana_pipetools/sequana_manager.py

@@ -26,7 +26,7 @@
 from tqdm.asyncio import tqdm
 
 from sequana_pipetools import get_package_version
-from sequana_pipetools.misc import url2hash
+from sequana_pipetools.misc import get_url_file_size, url2hash
 from sequana_pipetools.snaketools.profile import create_profile
 
 from .misc import Colors, PipetoolsException
@@ -568,6 +568,7 @@ def _download_zenodo_images(self):  # pragma: no cover
 
         count = 0
         files_to_download = []
+        total_size = 0
 
         # define the URLs and the output filename.
         for url in urls:
@@ -584,7 +585,7 @@ def _download_zenodo_images(self):  # pragma: no cover
 
             try:
                 Path(linkfile).symlink_to(f"{name}")
-            except FileExistsError:
+            except (FileExistsError, PermissionError):  # pragma: no cover
                 pass
 
             container = url.split("/")[-1]
@@ -596,6 +597,11 @@ def _download_zenodo_images(self):  # pragma: no cover
                 count += 1
                 logger.info(f"Preparing {url} for download")
 
+            total_size += get_url_file_size(url)
+        total_size /= 1024 * 1024
+        total_size = round(total_size)
+        logger.info(f"Total container size (Mb): {total_size}")
+
         try:  # try an asynchrone downloads
             multiple_downloads(files_to_download)
         except (KeyboardInterrupt, asyncio.TimeoutError):