Revert "chore: fix the ci to install the test requisites" (#264)

Author: ebetica

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ concurrency:
 
 jobs:
   test-precommit:
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-22.04-16core
 
     steps:
     - name: Checkout code
@@ -32,11 +32,20 @@ jobs:
         cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
     - name: Check formatting and typing
-      run: pixi run lint-all
+      run: |
+          set -e
+          # pyright seems to do something weird at initialization that causes it to error out
+          # We can ignore the first invocation here.
+          pyright esm/__init__.py || true
+          pre-commit install
+          env NODE_OPTIONS="--max-old-space-size=16384" pre-commit run --all-files --show-diff-on-failure
+          [ -z "$(git status --porcelain)" ] && true || (echo "❌❌❌ pre-commit hook failed! A few files changed ❌❌❌]" && git status --porcelain && false)
+          git reset --hard HEAD # test without the pre-commit changes
+      shell: pixi run bash -e {0}
 
 
   test-esm:
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-22.04-16core
 
     steps:
     - name: Checkout code
@@ -50,7 +59,10 @@ jobs:
         cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
     - name: Run tests
-      run: pixi run cov-test
+      run: |
+        set -o pipefail
+        pytest -v --junitxml=pytest.xml tests/ | tee pytest-coverage.txt
+      shell: pixi run bash -e {0}
 
     - name: Run Docker tests
       env:

.gitignore

@@ -2,4 +2,3 @@ esm.egg-info
 # pixi environments
 .pixi
 *.egg-info
-*.pyc

.pre-commit-config.yaml

@@ -9,7 +9,6 @@
 
 
 - [Installation ](#installation-)
-- [Available Models](#available-models-)
 - [ESM 3](#esm-3-)
   - [Quickstart for ESM3 Open](#esm3-quickstart-)
   - [ESM3 98B via Forge API](#esm3-forge)
@@ -34,31 +33,6 @@ To get started with ESM, install the python library using pip:
 pip install esm
 ```
 
-## Available Models <a name="available-models"></a>
-
-### ESM 3 Family
-
-| Model | Model Size | Release Date | Note |
-|-------|------------|--------------|------|
-| **Flagship Models** | | | Most users will be interested in using one of these models. |
-| esm3-large-2024-03 | 98B | 2024-03 | |
-| esm3-medium-2024-08 | 7B | 2024-08 | |
-| esm3-small-2024-08 | 1.4B | 2024-08 | |
-| **Published Models** | | | These models were used to generate all of the results in the ESM3 paper and are provided to facilitate reproducibility. |
-| esm3-large-2024-03 | 98B | 2024-03 | |
-| esm3-medium-2024-03 | 7B | 2024-03 | |
-| esm3-small-2024-03 | 1.4B | 2024-03 | |
-| **Experimental Models** | | | These models are provided for early use by researchers and are still under development. |
-| esm3-medium-multimer-2024-09 | 7B | 2024-09 | |
-
-### ESM C Models
-
-| Model | Model Size | Number of Layers | Release Date |
-|-------|------------|------------------|--------------|
-| esmc-6b-2024-12 | 6B | 80 | 2024-12 |
-| esmc-600m-2024-12 | 600M | 36 | 2024-12 |
-| esmc-300m-2024-12 | 300M | 30 | 2024-12 |
-
 ## ESM 3  <a name="esm3"></a>
 
 [ESM3](https://www.evolutionaryscale.ai/papers/esm3-simulating-500-million-years-of-evolution-with-a-language-model) is a frontier generative model for biology, able to jointly reason across three fundamental biological properties of proteins: sequence, structure, and function. These three data modalities are represented as tracks of discrete tokens at the input and output of ESM3. You can present the model with a combination of partial inputs across the tracks, and ESM3 will provide output predictions for all the tracks.

README.md

@@ -3,7 +3,7 @@ name = "esm"
 version = "3.2.1"
 description = "EvolutionaryScale open model repository"
 readme = "README.md"
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.10"
 license = {file = "LICENSE.txt"}
 
 authors = [
@@ -18,8 +18,6 @@ classifiers = [
   "Development Status :: 3 - Alpha",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
   "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
 ]
 
 dependencies = [
@@ -37,25 +35,9 @@ dependencies = [
   "attrs",
   "pandas",
   "cloudpathlib",
-  "httpx",
   "tenacity",
-  "zstd",
-  "ipywidgets",
-  "py3dmol",
-  "pydssp",
-  "boto3",
-  "pygtrie",
-  "dna_features_viewer",
-  "flash-attn @ https://github.com/Dao-AILab/flash-attention/releases/download/v2.8.1/flash_attn-2.8.1+cu12torch2.7cxx11abiFALSE-cp312-cp312-linux_x86_64.whl"
+  "zstd"
 ]
-# Pytest
-[tool.pytest.ini_options]
-addopts = """
-  --cov=esm
-	--cov-report term-missing:skip-covered
-	-n auto
-	--ignore=tests/oss_pytests/test_oss_client.py
-"""
 
 [tool.setuptools]
 package-dir = {"" = "."}
@@ -70,76 +52,18 @@ esm = ["data/*"]
 
 [tool.pixi.project]
 channels = ["conda-forge"]
-platforms = ["linux-64", "osx-arm64"]
+platforms = ["linux-64"]
 
 # These are build dependencies, to ensure pip support, keep run-time deps above in `dependencies`
 [tool.pixi.dependencies]
 pkg-config = "*"
 cmake = "*"
 pip = "*"
 twine = "*"
-python = "3.12.*"
 
 [tool.pixi.pypi-dependencies]
 esm = { path = ".", editable = true }
 
 [tool.pixi.tasks]
 build-wheel = "python -m pip wheel --no-deps -w dist ."
 upload-wheel = "python -m twine upload --repository pypi"
-
-[tool.pixi.feature.dev.dependencies]
-matplotlib = "*"
-pre-commit = "*"
-pytest = "*"
-pytest-cov = "*"
-seaborn = "*"
-pyright = "==1.1.399"
-
-[tool.pixi.feature.dev.tasks]
-lint-all = "pre-commit run --all-files --show-diff-on-failure"
-cov-test = "pytest -v --junitxml=pytest.xml --cov=esm"
-
-[tool.pixi.environments]
-default = {features = [], solve-group = "default"}
-dev = {features = ["dev"], solve-group = "default"}
-
-[tool.ruff]
-extend-include = ["*.ipynb"]
-
-[tool.ruff.lint]
-# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`), sort imports ('I')
-select = ["E4", "E7", "E9", "F", "I"]
-ignore = [
-    # allow variable == False (tensors should do this)
-    "E712",
-    # allow assigning of lambdas
-    "E731",
-    # Allow ambiguous variables, e.g. we use O for oxygen
-    "E741",
-    # Ignore errors from jaxtyping hints
-    # https://docs.kidger.site/jaxtyping/faq/#flake8-or-ruff-are-throwing-an-error
-    "F722",
-    # TODO: Fix the few offenders in a follow up PR
-    "E721",
-]
-
-[tool.ruff.lint.isort]
-split-on-trailing-comma = false
-known-third-party = ["wandb"]
-
-[tool.ruff.format]
-skip-magic-trailing-comma = true
-docstring-code-format = true
-docstring-code-line-length = "dynamic"
-
-[tool.isort]
-known_third_party = ["wandb"]
-
-[tool.pyright]
-root = ['.']
-useLibraryCodeForTypes = true
-reportPrivateImportUsage = false
-typeCheckingMode = "basic"
-
-[tool.importlinter]
-root_package = "esm"