Feature/improve speed and limit memory (#11)

.gitlab-ci.yml

@@ -0,0 +1,43 @@
+image: python:3.10.5
+
+
+variables:
+  PIP_CACHE_DIR: "${CI_PROJECT_DIR}/.cache/pip"
+
+stages:
+  - publish
+
+cache:
+  key: "${CI_COMMIT_REF_SLUG}"
+  paths:
+    - .cache/pip
+    - .venv
+
+.with_poetry:
+  before_script:
+    - pip install poetry
+    - poetry --version
+    - poetry config virtualenvs.in-project true
+    - poetry install
+
+license_dump:
+  extends: .with_poetry
+  stage: publish
+  script:
+    - poetry run pip-licenses --from=mixed --order=license --with-system --format=csv  > licenses.csv
+  artifacts:
+    paths:
+      - licenses.csv
+    expire_in: 1 week
+
+publish:
+  extends: .with_poetry
+  stage: publish
+  rules:
+    - if: '$CI_COMMIT_TAG != null'
+  script:
+    - poetry config repositories.gitlab https://gitlab.com/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
+    - poetry config http-basic.gitlab gitlab-ci-token ${CI_JOB_TOKEN}
+    - poetry build
+    - poetry publish -r gitlab
+

mokapot/__init__.py

@@ -15,11 +15,11 @@
     except DistributionNotFound:
         pass
 
-from .dataset import LinearPsmDataset
+from .dataset import LinearPsmDataset, OnDiskPsmDataset, read_file
 from .model import Model, PercolatorModel, save_model, load_model
 from .brew import brew
 from .parsers.pin import read_pin, read_percolator
 from .parsers.pepxml import read_pepxml
 from .parsers.fasta import read_fasta, make_decoys, digest
 from .writers import to_flashlfq, to_txt
-from .confidence import LinearConfidence, plot_qvalues
+from .confidence import LinearConfidence, plot_qvalues, assign_confidence