Release 1.5.0 (#347)

* GitHub Actions(deps): bump actions/checkout from 4 to 5 (#325)

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* pip(deps-dev): bump mkdocs-material from 9.6.16 to 9.6.18 (#326)

Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.6.16 to 9.6.18.
- [Release notes](https://github.com/squidfunk/mkdocs-material/releases)
- [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG)
- [Commits](squidfunk/mkdocs-material@9.6.16...9.6.18)

---
updated-dependencies:
- dependency-name: mkdocs-material
  dependency-version: 9.6.18
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* pip(deps-dev): bump mkdocstrings-python from 1.16.12 to 1.18.2 (#327)

Bumps [mkdocstrings-python](https://github.com/mkdocstrings/python) from 1.16.12 to 1.18.2.
- [Release notes](https://github.com/mkdocstrings/python/releases)
- [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md)
- [Commits](mkdocstrings/python@1.16.12...1.18.2)

---
updated-dependencies:
- dependency-name: mkdocstrings-python
  dependency-version: 1.18.2
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

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* pip(deps-dev): bump pyright from 1.1.403 to 1.1.404 (#328)

Bumps [pyright](https://github.com/RobertCraigie/pyright-python) from 1.1.403 to 1.1.404.
- [Release notes](https://github.com/RobertCraigie/pyright-python/releases)
- [Commits](RobertCraigie/pyright-python@v1.1.403...v1.1.404)

---
updated-dependencies:
- dependency-name: pyright
  dependency-version: 1.1.404
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* bump workflow (#329)

Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch>

* pip(deps-dev): bump mkdocs-material from 9.6.18 to 9.6.19 (#333)

Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.6.18 to 9.6.19.
- [Release notes](https://github.com/squidfunk/mkdocs-material/releases)
- [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG)
- [Commits](squidfunk/mkdocs-material@9.6.18...9.6.19)

---
updated-dependencies:
- dependency-name: mkdocs-material
  dependency-version: 9.6.19
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* pip(deps-dev): bump pyright from 1.1.404 to 1.1.405 (#332)

Bumps [pyright](https://github.com/RobertCraigie/pyright-python) from 1.1.404 to 1.1.405.
- [Release notes](https://github.com/RobertCraigie/pyright-python/releases)
- [Commits](RobertCraigie/pyright-python@v1.1.404...v1.1.405)

---
updated-dependencies:
- dependency-name: pyright
  dependency-version: 1.1.405
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* GitHub Actions(deps): bump actions/setup-python from 5 to 6 (#331)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* pip(deps): bump pydantic from 2.11.7 to 2.11.9 (#340)

Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.11.7 to 2.11.9.
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/v2.11.9/HISTORY.md)
- [Commits](pydantic/pydantic@v2.11.7...v2.11.9)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-version: 2.11.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* feat: submit `.bam` and Loculus Config (#337)

Adds nucleotide alignment file (.bam) submission functionality to the W-ASAP Loculus workflow and updates metadata field configuration. The changes enable submitting both processed data files and alignment files to Loculus while updating the sr2silo dependency.

- Adds nucleotide alignment file parameter to the submission workflow
- Updates sr2silo from version 1.3.0 to 1.4.0
- Modifies Loculus client to handle two-file uploads with proper file mapping

* pip(deps-dev): bump black from 25.1.0 to 25.9.0 (#343)

Bumps [black](https://github.com/psf/black) from 25.1.0 to 25.9.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@25.1.0...25.9.0)

---
updated-dependencies:
- dependency-name: black
  dependency-version: 25.9.0
  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>

* pip(deps-dev): bump mkdocs-material from 9.6.19 to 9.6.20 (#344)

Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.6.19 to 9.6.20.
- [Release notes](https://github.com/squidfunk/mkdocs-material/releases)
- [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG)
- [Commits](squidfunk/mkdocs-material@9.6.19...9.6.20)

---
updated-dependencies:
- dependency-name: mkdocs-material
  dependency-version: 9.6.20
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* remove .env usage (#342)

Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch>

* feat: revision (#346)

Adds a duplicate submission prevention feature to avoid resubmitting the same sample_ids to the Loculus W-ASAP instance. The implementation includes checking for existing released samples before submission and providing an option to override this behavior.

- Added duplicate detection logic to check existing sample_ids before submission
- Implemented enhanced error tracking with full traceback logging
- Added new functions to fetch and process released samples from the Loculus API

* bump (#348)

Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch>

* fix: amino acid position shifted by +1 (#350)

- turned out this was a double bug
- for one positions taken equal to offsets
- but offset = position - 1
- lead to a shift in amino acids and nuclitides by  +1
- was compensated by 0-indexing error of -bam in pysam
- corrected bam_to_fastq_handle_indels()

Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Gordon J. Köhn <gordon.koehn@dbsse.ethz.ch>

Author: 3 people

.env.example

@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v5
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
           cache: "pip"

.github/workflows/docs.yml

@@ -18,7 +18,7 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.11'
           cache: 'pip'

.github/workflows/test.yml

@@ -102,7 +102,6 @@ celerybeat.pid
 *.sage.py
 
 # Environments
-.env
 .venv
 env/
 venv/

.gitignore

@@ -1,6 +1,6 @@
 # conda recipe
 {% set name = "sr2silo" %}
-{% set version = "1.4.0" %}
+{% set version = "1.5.0" %}
 
 package:
   name: {{ name|lower }}
@@ -38,7 +38,6 @@ requirements:
     - pysam >=0.23.0
     - requests >=2.25.0
     - moto >=5.0.22
-    - python-dotenv >=1.0.0
 
 test:
   imports:

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "sr2silo"
-version = "1.4.0"
+version = "1.5.0"
 description = "ETL tool for importing short-read sequencing data into SILO database (v0.8.0+), powering Loculus."
 authors = ["Gordon Julian Koehn <gordon.koehn@dbsse.ethz.ch>"]
 readme = "README.md"
@@ -20,7 +20,6 @@ zstandard = "^0.23.0"
 typer = "^0.15.1"
 biopython = "^1.83"
 pysam = "^0.23.0"
-python-dotenv = "^1.0.0"
 
 
 [tool.poetry.group.dev.dependencies]

poetry.lock

@@ -8,18 +8,6 @@
 import sys
 from pathlib import Path
 
-from dotenv import load_dotenv
-
-# Load .env file from the project root if it exists
-env_path = Path(__file__).parent.parent.parent / ".env"
-if env_path.exists():
-    load_dotenv(dotenv_path=env_path)
-    logging.info(f"Loaded environment variables from {env_path} using python-dotenv")
-else:
-    logging.debug(
-        f"No .env file found at {env_path}, using only system environment variables"
-    )
-
 
 def is_ci_environment() -> bool:
     """Check if running in a CI environment."""
@@ -92,7 +80,16 @@ def get_organism() -> str:
     Returns:
         str: The organism identifier (e.g., 'sc2', 'sars-cov-2')
     """
-    return os.getenv("ORGANISM", "sc2")
+    try:
+        organism = os.getenv("ORGANISM")
+        if organism:
+            return organism
+        else:
+            logging.error("ORGANISM environment variable is not set.")
+            sys.exit(1)
+    except Exception as e:
+        logging.error(f"Error retrieving ORGANISM from environment: {e}")
+        sys.exit(1)
 
 
 def get_timeline_file(default: Path | str | None = None) -> Path | None: