diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 000000000..887a2c18f
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
diff --git a/.gitignore b/.gitignore
index 4e4836886..feeca27d8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,3 +16,10 @@ cutlass/
 
 # User-specific pre-commit settings
 .pre-commit-config.yaml
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
+# uv environments
+.venv/
diff --git a/docs/source/Installation.md b/docs/source/Installation.md
index 96db2da83..c0c245957 100644
--- a/docs/source/Installation.md
+++ b/docs/source/Installation.md
@@ -30,8 +30,34 @@ to install GPU accelerated {doc}`cuEquivariance attention kernels <kernels>`, us
 pip install openfold3[cuequivariance]
 ```
 
+### Modern conda environments with pixi
+
+OpenFold3 can now be installed in conda environments with [pixi](https://pixi.prefix.dev/latest/index.html).
+
+First [install pixi](https://pixi.prefix.dev/latest/installation/)
+
+```shell
+# Do this once and enjoy pixi for all your future projects!
+curl -fsSL https://pixi.sh/install.sh | sh
+# Then restart your shell and optionally install pixi completions
+```
+
+You can simply run openfold in one of the provided environments with pixi:
+```shell
+pixi run -e openfold3-cpu setup_openfold
+pixi run -e openfold3-cpu run_openfold
+```
+
+We provide the following environments:
+ - openfold3-cpu (linux-64, linux-aarch64, osx-64,osx-arm64)
+ - openfold3-cuda12 and openfold-cuda13 (linux-64, linux-aarch64) 
+
+For more information, including rationale, tips and tricks, see [Modern Conda Environments with Pixi](./modern-conda-environments-with-pixi.md).
+
 ### Environment variables
 
+> **Note:** This may need a revision given the pixi managed envs above (JD).
+
 OpenFold may need a few environment variables set so CUDA, compilation, and JIT-built extensions can be found correctly. 
 
 - `CUDA_HOME` should point to the CUDA installation. On many HPC clusters you will this can be set by loading the appropriate toolchain using environment modules, for example `module load cuda`.  If you do not set this you will likely get a `No such file or directory: '/usr/local/cuda/bin/nvcc'` error. 
@@ -54,7 +80,6 @@ OpenFold may need a few environment variables set so CUDA, compilation, and JIT-
     - Example: `export LIBRARY_PATH="$(echo "$CUDA_HOME" | sed 's|/cuda/|/math_libs/|')/targets/sbsa-linux/lib:${LIBRARY_PATH:-}"`
 
 
-
 ### OpenFold3 Docker Image
 
 #### Dockerhub
diff --git a/docs/source/modern-conda-environments-with-pixi.md b/docs/source/modern-conda-environments-with-pixi.md
new file mode 100644
index 000000000..73b516514
--- /dev/null
+++ b/docs/source/modern-conda-environments-with-pixi.md
@@ -0,0 +1,3 @@
+# Modern OpenFold conda environments with pixi
+
+
diff --git a/examples/example_runner_yamls/osx.yaml b/examples/example_runner_yamls/osx.yaml
new file mode 100644
index 000000000..b40e4432e
--- /dev/null
+++ b/examples/example_runner_yamls/osx.yaml
@@ -0,0 +1,14 @@
+model_update:
+  presets: 
+    - "predict"
+    - "pae_enabled"  # if using PAE enabled model
+    # - "low_mem"  # for lower memory systems
+  custom:
+    settings:
+      memory:
+        eval:
+          # otherwise the current default is wrongly to use deepspeed, even if not available
+          use_deepspeed_evo_attention: false
+
+data_module_args:
+  num_workers: 1
diff --git a/openfold3/__init__.py b/openfold3/__init__.py
index 498f8364c..a0db446c7 100644
--- a/openfold3/__init__.py
+++ b/openfold3/__init__.py
@@ -19,8 +19,6 @@
 import gemmi
 from packaging import version
 
-from . import hacks  # noqa: F401
-
 if version.parse(gemmi.__version__) >= version.parse("0.7.3"):
     gemmi.set_leak_warnings(False)
 
@@ -32,3 +30,4 @@
     # This has weird effects with hanging if libaio is not installed and can
     # cause restart errors if run is preempted in the middle of autotuning
     deepspeed.HAS_TRITON = False
+    # FIXME: do we need this? it is really invasive with other potential users of DS
diff --git a/openfold3/core/data/framework/data_module.py b/openfold3/core/data/framework/data_module.py
index e0b858918..8956c5d63 100644
--- a/openfold3/core/data/framework/data_module.py
+++ b/openfold3/core/data/framework/data_module.py
@@ -42,6 +42,9 @@
 import dataclasses
 import enum
 import logging
+import multiprocessing
+import platform
+import sys
 import warnings
 from functools import partial
 from typing import Any
@@ -148,14 +151,78 @@ def get_config_for_mode(self, mode: DatasetMode) -> "MultiDatasetConfig":
         return self.get_subset(datasets_stage_mask)
 
 
+
 class DataModuleConfig(BaseModel):
     datasets: list[SerializeAsAny[BaseModel]]
     batch_size: int = 1
     num_workers: int = 0
     num_workers_validation: int = 0
+    multiprocessing_context: str = "openfold-default"
     data_seed: int = 42
     epoch_len: int = 1
 
+    @staticmethod
+    def safe_multiprocessing_context(
+            multiprocessing_context: str | None, num_workers: int
+    ) -> str | None:
+        """
+        Returns multiprocessing start methods with safer/sensible defaults:
+          - fork when using MPS
+          - forkserver for linux, matching the new 3.14 default
+          - default otherwise
+
+        For general info on risks and defaults across platformas and python versions see:
+          https://docs.pytorch.org/docs/stable/data.html#torch.utils.data.DataLoader
+          https://docs.pytorch.org/docs/stable/notes/multiprocessing.html#multiprocessing-poison-fork-note
+          https://docs.python.org/3/library/multiprocessing.html#contexts-and-start-methods
+        """
+
+        # Do not bother if not using multiprocessing
+        if num_workers == 0:
+            return None
+
+        # Set safe defaults
+        if multiprocessing_context == "openfold-default":
+
+            # Use fork to create processes when using MPS. See:
+            #  - https://github.com/pytorch/pytorch/issues/70344
+            #  - https://github.com/pytorch/pytorch/issues/87688
+            if platform.system() == "Darwin" and torch.backends.mps.is_available():
+                return "fork"
+
+            # Use forkserver in linux
+            # Backports the new python 3.14 default in previous python versions.
+            # An alternative for further safety would be "spawn". Avoid "fork".
+            # See: https://github.com/python/cpython/issues/84559
+            if platform.system() == "Linux":
+                return "forkserver"
+
+            # Use the platform default otherwise - "spawn" at the time of writing
+            return multiprocessing.get_start_method()
+
+        # Warn about unsafe defaults
+        else:
+            if platform.system() == "Darwin" and torch.backends.mps.is_available():
+                if multiprocessing_context != "fork":
+                    logger.warning(
+                        f"Using multiprocessing context {multiprocessing_context} on MPS may cause "
+                        "issues. Consider using 'fork' or 'openfold-default' (which resolves to 'fork' on MPS).",
+                        stacklevel=2,
+                    )
+            if platform.system() == "Linux":
+                dangerous_start_method = (
+                    multiprocessing_context == "fork" or
+                    multiprocessing_context is None and sys.version_info < (3, 14)
+                )
+                if dangerous_start_method:
+                    logger.warning(
+                        "Using 'fork' multiprocessing context in linux may cause issues. Consider using "
+                        "'spawn', 'forkserver' or 'openfold-default' (which resolves to 'forkserver' on linux).",
+                        stacklevel=2,
+                    )
+
+        return multiprocessing_context
+
 
 class DataModule(pl.LightningDataModule):
     """A LightningDataModule class for organizing Datasets and DataLoaders."""
@@ -167,6 +234,7 @@ def __init__(self, data_module_config: DataModuleConfig) -> None:
         self.batch_size = data_module_config.batch_size
         self.num_workers = data_module_config.num_workers
         self.num_workers_validation = data_module_config.num_workers_validation
+        self.multiprocessing_context = data_module_config.multiprocessing_context
         self.data_seed = data_module_config.data_seed
         self.next_data_seed = data_module_config.data_seed
         self.epoch_len = data_module_config.epoch_len
@@ -433,8 +501,17 @@ def generate_dataloader(self, mode: DatasetMode, sampler: Sampler | None = None)
         # instead of pl.seed_everything(workers=True), so this function is
         # passed explicitly here.
         worker_init_fn = partial(pl_worker_init_function, rank=self.global_rank)
+
+        # Set a sensible default for multiprocesssing start method
+        # depending on platform and python version.
+        multiprocessing_context = DataModuleConfig.safe_multiprocessing_context(
+            self.multiprocessing_context, num_workers
+        )
+
         logger.debug(
-            f"Creating {mode} dataloader: num_workers={num_workers}, "
+            f"Creating {mode} dataloader: "
+            f"num_workers={num_workers}, "
+            f"multiprocessing_context={multiprocessing_context}, "
             f"rank={self.global_rank}."
         )
         return DataLoader(
@@ -445,6 +522,7 @@ def generate_dataloader(self, mode: DatasetMode, sampler: Sampler | None = None)
             collate_fn=openfold_batch_collator,
             generator=self.generators[mode],
             worker_init_fn=worker_init_fn,
+            multiprocessing_context=multiprocessing_context,
         )
 
     def train_dataloader(self) -> DataLoader:
diff --git a/openfold3/core/data/pipelines/featurization/conformer.py b/openfold3/core/data/pipelines/featurization/conformer.py
index 7d0f41add..711d9593e 100644
--- a/openfold3/core/data/pipelines/featurization/conformer.py
+++ b/openfold3/core/data/pipelines/featurization/conformer.py
@@ -108,6 +108,10 @@ def featurize_reference_conformers_of3(
             coords = conf.GetAtomPosition(atom.GetIdx())
             mol_ref_mask.append(int(atom.GetBoolProp("annot_used_atom_mask")))
             mol_ref_pos.append(coords)
+            # Some PyPI installations crash here due to ABI mismatch between RDKit and PyTorch
+            # Leaving a quick fix commented (beware, moving into slow python land)
+            # Remove if nobody else hits the problem
+            # mol_ref_pos.append([coords.x, coords.y, coords.z])
 
             # Atom elements (0-indexed)
             element_symbol = atom.GetSymbol()
diff --git a/openfold3/core/model/primitives/attention.py b/openfold3/core/model/primitives/attention.py
index 4842c16de..7b3f8eb70 100644
--- a/openfold3/core/model/primitives/attention.py
+++ b/openfold3/core/model/primitives/attention.py
@@ -507,11 +507,6 @@ def _deepspeed_evo_attn(
         biases:
             List of biases that broadcast to [*, H, Q, K]
     """
-    from openfold3 import hacks
-
-    hacks.prep_deepspeed()
-    hacks.prep_cutlass()
-
     if not ds4s_is_installed:
         raise ValueError(
             "_deepspeed_evo_attn requires that DeepSpeed be installed "
diff --git a/openfold3/hacks.py b/openfold3/hacks.py
deleted file mode 100644
index 189b7d945..000000000
--- a/openfold3/hacks.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import importlib
-import os
-from pathlib import Path
-
-PLACEHOLDER_PATH = "placeholder"
-
-
-def prep_deepspeed():
-    # deepspeed requires the envvar set, but doesn't care about value
-    # if already set (i.e. local cutlass setup), retain existing value
-    os.environ["CUTLASS_PATH"] = os.environ.get("CUTLASS_PATH", PLACEHOLDER_PATH)
-
-
-def prep_cutlass():
-    cutlass_lib_is_installed = importlib.util.find_spec("cutlass_library") is not None
-    cutlass_path = Path(os.environ.get("CUTLASS_PATH", PLACEHOLDER_PATH))
-
-    # TODO: This check is for backward compatibility with the old local cutlass setup.
-    #  Remove this and use pip installation only in the future.
-    if not cutlass_lib_is_installed:
-        if not cutlass_path.exists():
-            raise OSError(
-                "CUTLASS_PATH environment variable is not set to a valid path, "
-                "and cutlass_library is not installed. Please install nvidia-cutlass"
-                "via pip or set CUTLASS_PATH to the root of a local cutlass clone."
-            )
-
-        return
-
-    # apparently need to set the headers for cutlass
-    import cutlass_library
-
-    headers_dir = Path(cutlass_library.__file__).parent / "source/include"
-    cpath = os.environ.get("CPATH", "")
-    # TODO: technically, this test should be a little fancier
-    if str(headers_dir.resolve()) not in cpath:
-        if cpath:
-            cpath += ":"
-
-        os.environ["CPATH"] = cpath + str(headers_dir.resolve())
diff --git a/openfold3/tests/__init__.py b/openfold3/tests/__init__.py
index 0e41df04b..090c0f6b3 100644
--- a/openfold3/tests/__init__.py
+++ b/openfold3/tests/__init__.py
@@ -14,8 +14,6 @@
 
 import importlib
 
-from openfold3 import hacks  # noqa: F401
-
 if importlib.util.find_spec("deepspeed") is not None:
     import deepspeed
 
@@ -23,3 +21,4 @@
     # This is a hack to prevent deepspeed from doing the triton matmul autotuning
     # I'm not sure why it's doing this by default, but it's causing the tests to hang
     deepspeed.HAS_TRITON = False
+    # FIXME: potentially too invasive with other libraries, see also comments up about libaio
diff --git a/openfold3/tests/scripts/data_preprocessing/test_preparse_alignments_of3.py b/openfold3/tests/scripts/data_preprocessing/test_preparse_alignments_of3.py
index 318e5fd2b..7a0253c08 100644
--- a/openfold3/tests/scripts/data_preprocessing/test_preparse_alignments_of3.py
+++ b/openfold3/tests/scripts/data_preprocessing/test_preparse_alignments_of3.py
@@ -62,7 +62,7 @@ def test_preparse_databases(self, cli_runner, tmp_path):
 
         # Check that npz files were created for both chains
         npz_files = list(tmp_path.glob("*.npz"))
-        assert [f.name for f in npz_files] == ["2q2k_B.npz", "2q2k_A.npz"]
+        assert set([f.name for f in npz_files]) == {"2q2k_B.npz", "2q2k_A.npz"}
 
         # Check contents of one npz file
         npz_data = np.load(tmp_path / "2q2k_A.npz", allow_pickle=True)
diff --git a/openfold3/tests/test_lmdb.py b/openfold3/tests/test_lmdb.py
index 29f367b63..7fab2e329 100644
--- a/openfold3/tests/test_lmdb.py
+++ b/openfold3/tests/test_lmdb.py
@@ -66,7 +66,7 @@ def test_lmdb_roundtrip(self, tmp_path):
 
         # Create LMDB
         test_lmdb_dir = tmp_path / "test_lmdb"
-        map_size = 20 * 1024
+        map_size = 200 * 1024
         convert_datacache_to_lmdb(test_config_json, test_lmdb_dir, map_size)
 
         # read lmdb
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 000000000..3bfa8b8ba
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,21374 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://conda.anaconda.org/bioconda/
+    indexes:
+    - https://pypi.org/simple
+    options:
+      pypi-prerelease-mode: if-necessary-or-explicit
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-hf4e2dac_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+      - pypi: https://files.pythonhosted.org/packages/05/a4/b12881e24700e1f4e5d54ff49f3a64bfab9115faf18ad84eb75f654b0871/pixi_to_conda_lock-0.4.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/5a/86/6e0202ddd5ffc1c9cb1be80c9981a67061413e05ab6073939fa9c9dc0821/py_rattler-0.23.2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/88/f9/16491d7ed2a919954993e48aa941b200f38040928474c9e85ea9e64222c3/pyyaml-6.0.3-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
+      linux-aarch64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/icu-78.3-hcab7f73_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.4-hfae3067_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.2-he30d5cf_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libmpdec-4.0.0-he30d5cf_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.52.0-h10b116e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-15.2.0-hef695bb_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.41.3-h1022ec0_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.1-h546c87b_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.3-hb06a95a_101_cp314.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-hb682ff5_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
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+  license_family: MIT
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+  version: 1.23.0
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+  license: MIT
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 000000000..cd5a8393b
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,450 @@
+#
+# This is a pixi (https://pixi.sh) manifest to manage environments for OpenFold-3.
+# TL;DR:
+#   pixi run run_openfold
+#
+# Installing pixi
+# ---------------
+# If you have not pixi installed, please follow the instructions here:
+#   https://pixi.sh/latest/installation/
+# Which in linux boils down to run:
+#   curl -fsSL https://pixi.sh/install.sh | sh
+# Optionally, please install shell completions.
+# Then restart your shell.
+#
+# Platforms and hardware support
+# ------------------------------
+# We support linux-64, linux-aarch64, osx-64 and osx-arm64 platforms and provide the following environments:
+#   - default: an environment to maintain the rest of environments
+#   - openfold3-cpu: base environment without CUDA, to enable developing without GPU
+#   - openfold3-cuda12 and openfold-cuda13: environments with cuda, deepspeed and cuequivariance
+#   - openfold3-cuda12-pypi and openfold-cuda13-pypi: environments with python and cuda from conda,
+#                                                     everything else from pypi
+#                                                     keeping the environments as sane and consistent as possible
+#                                                     (useful if requiring deps not yet in conda-forge)
+#
+# The current environments pass all inference tests available in each platform.
+# (aarch64 and osx-64 are untested at the moment).
+# The GPU versions work at least from NVIDIA Ampere to Blackwell microarchitectures
+# +---------------+------------+------------+------------+------------+
+# | Linux         | x64        | x64        | aarch64    | aarch64    |
+# |               | conda      | pypi       | conda      | pypi       |
+# +---------------+------------+------------+------------+------------+
+# | A100 cuda12   | works      | works      | to test    | to test    |
+# | A100 cuda13   | works      | works      | to test    | to test    |
+# | H100 cuda12   | to test    | to test    | to test    | to test    |
+# | H100 cuda13   | to test    | to test    | to test    | to test    |
+# | B300 cuda12   | works      | works      | to test    | to test    |
+# | B300 cuda13   | works      | works      | to test    | to test    |
+# | GB10 cuda12   | n/a        | n/a        | works      | works      |
+# | GB10 cuda13   | n/a        | n/a        | works      | works      |
+# | CPU           | works      | n/a        | to test    | n/a        |
+# +---------------+------------+------------+------------+------------+
+#    * works = "works for me"
+#    * to test = "have not tried yet, but environment resolves"
+#
+# Using the environments
+# ----------------------
+# Change to the openfold-3 directory and run any command using the pixi shim.
+#   pixi run -e openfold3-cuda12 pytest -v .
+#   pixi run run_openfold
+#
+# If you want to run out of the openfold-3 environment, there are multiple options:
+#  use `pixi shell` to allow running out of the directory and saving prefixing with "pixi run".
+#  use detached environments or specify a different manifest location
+#  hold tight for pixi's environment registry feature: https://github.com/prefix-dev/pixi/pull/5277
+#
+# If you prefer to use conda, the environments can be exported to regular conda YAMLs:
+#   pixi run export-conda openfold3-cuda12 linux-64
+#   pixi run export-conda-all
+# Note that at the moment this does not export environment variable definitions
+# which we use for isolating deepspeed extension building.
+#
+# Also conda-lock files can be exported
+#   pixi run export-conda openfold3-cuda12
+#   pixi run export-conda-all
+# Note that all environment variables (skip cutlass detection and deepspeed build isolation)
+# need to be setup manually for these environments. We hope that soon we will be able
+# to export the whole environment variable setup together with these conda environments.
+#
+
+[workspace]
+name = "openfold3"
+authors = ["OpenFold Team <support@openfold.io>"]
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64"]
+version = "0.4.0"
+
+# as we use task.default-environment
+# hoping for environment markers to also come to conda dependencies, as it would help simplifying this toml
+# https://github.com/prefix-dev/pixi/blob/main/CHANGELOG.md#-highlights-1
+requires-pixi = ">=0.64"
+
+# --- Environments
+
+[environments]
+default = { features = [ "python", "pixi-to-conda-lock" ] }
+openfold3-cpu = { no-default-feature = true, features = [
+    "python",
+    "openfold3-cpu",
+    "pytorch-conda",
+    "openfold3-editable",
+    "tests"
+] }
+openfold3-cuda12 = { no-default-feature = true, features = [
+    "python",
+    "openfold3-cpu",
+    "cuda12",
+    "pytorch-conda-cuda",
+    "deepspeed",
+    "deepspeed-build",
+    "cuequivariance-cuda12",
+    "openfold3-editable",
+    "tests"
+] }
+openfold3-cuda13 = { no-default-feature = true, features = [
+    "python",
+    "openfold3-cpu",
+    "cuda13",
+    "pytorch-conda-cuda",
+    "deepspeed",
+    "deepspeed-build",
+    "cuequivariance-cuda13",
+    "openfold3-editable",
+    "tests"
+] }
+openfold3-cuda12-pypi = { no-default-feature = true, features = [
+    "python",
+    "cuda12",
+    "pytorch-pypi-cuda12",
+    "not-in-pypi",
+    "deepspeed-build",
+    "cuequivariance-cuda12",
+    "openfold3-editable-full",
+    "tests"
+] }
+openfold3-cuda13-pypi = { no-default-feature = true, features = [
+    "python",
+    "cuda13",
+    "pytorch-pypi-cuda13",
+    "not-in-pypi",
+    "deepspeed-build",
+    "cuequivariance-cuda13",
+    "openfold3-editable-full",
+    "tests"
+] }
+
+# Maybe we should have solve-groups, but how to conciliate between e.g. cu12 and cu13?
+# N.B. at the moment all these are editable installs
+
+# --- CPU dependencies (excluding torch-related)
+
+# --- OpenFold3 in editable mode
+# The goal here would be to avoid getting anything installed from pypi in this step.
+# We should be able to provide envs with non-editable installs (e.g., prod vs devel)
+
+[feature.openfold3-editable.pypi-dependencies]
+openfold3 = { path = ".", editable = true }
+
+[feature.openfold3-editable-full.target.linux.dependencies]
+# No compatible wheels for cuequivariance<0.8, python 3.14 and linux-aarch64
+python = "<3.14"
+
+[feature.openfold3-editable-full.pypi-dependencies]
+openfold3 = { path = ".", editable = true, extras = ["deepspeed", "dev"] }
+
+#[feature.kalign.pypi-dependencies]
+#kalign-python = "*"
+
+[feature.not-in-pypi.target.linux.dependencies]
+hmmer = "*"
+hhsuite = "*"
+# func_timeout does not get resolved by pixi from pypi if running pixi in osx
+#   see: https://pypi.org/project/func-timeout/#description
+# if we remove this, we fail to solve the environment with:
+#   Error:   × failed to solve the pypi requirements of environment 'openfold3-cuda12-pypi' for platform 'linux-aarch64'
+#    ╰─▶ build dispatch initialization failed: there is no compatible Python interpreter for 'osx-arm64'
+func_timeout = "*"
+
+
+[feature.python.dependencies]
+python = "*"
+# Enable evil post-modifications, also pixi-to-conda-lock
+# (pixi joint pypi/conda resolution is too good and does not allow sometimes necessary evil)
+pip = "*"
+
+
+[feature.openfold3-cpu.dependencies]
+
+# Explicit basics that could get anyway installed
+numpy = "*"
+scipy = "*"
+pandas = "*"
+
+# --- More ML
+ml-collections = "*"
+
+# --- Handling molecules
+rdkit = "*"
+biotite = ">=1.6"
+pdbeccdutils = "*"
+
+# --- Bioinformatics & Workflows
+hmmer = "*"
+hhsuite = "*"
+snakemake = "*"
+
+# --- Misc
+pyyaml = "*"
+ijson = "*"
+memory_profiler = "*"
+wandb = "*"
+func_timeout = "*"
+tqdm = "*"
+typing-extensions = "*"
+python-lmdb = "*"
+
+# --- Downloading stuff
+requests = "*"
+awscli = "*"
+awscrt = "*"
+boto3 = "*"
+aria2 = "*"
+
+# --- Testing
+pytest = "*"
+pytest-xdist = "*"
+pytest-cov = "*"
+pytest-benchmark = "*"
+
+# --- Dev and documentation optionals
+# We do not put on a feature to avoid combinatorial explosion.
+ruff = "*"
+sphinx = "*"
+myst-parser = "*"
+furo = "*"
+
+[feature.openfold3-cpu.target.linux-64.dependencies]
+mkl = "*"
+
+# --- Pytorch & Cuda
+
+[feature.pytorch-conda-cuda.dependencies]
+pytorch-lightning = "*"
+pytorch-gpu = "*"
+
+[feature.pytorch-conda.dependencies]
+pytorch-lightning = "*"
+pytorch = "*"
+
+[feature.pytorch-pypi-cuda12.pypi-dependencies]
+pytorch-lightning = "*"
+torch = { version = "*", index = "https://download.pytorch.org/whl/cu129" }
+
+[feature.pytorch-pypi-cuda13.pypi-dependencies]
+pytorch-lightning = "*"
+torch = { version = "*", index = "https://download.pytorch.org/whl/cu130" }
+
+[feature.cuda12]
+
+  platforms = ["linux-64", "linux-aarch64"]
+
+  [feature.cuda12.system-requirements]
+  cuda = "12.0"
+
+  [feature.cuda12.dependencies]
+  cuda-version = ">=12,<13"
+
+  [feature.cuda12.activation]
+  env.TRITON_PTXAS_PATH = "$CONDA_PREFIX/bin/ptxas"
+  env.TRITON_PTXAS_BLACKWELL_PATH = "$TRITON_PTXAS_PATH"
+
+[feature.cuda13]
+
+  platforms = ["linux-64", "linux-aarch64"]
+
+  [feature.cuda13.system-requirements]
+  cuda = "13.0"
+
+  [feature.cuda13.dependencies]
+  cuda-version = ">=13,<14"
+
+  [feature.cuda13.activation]
+  env.TRITON_PTXAS_PATH = "$CONDA_PREFIX/bin/ptxas"
+  env.TRITON_PTXAS_BLACKWELL_PATH = "$TRITON_PTXAS_PATH"
+
+
+# --- DeepSpeed
+
+[feature.deepspeed]
+
+  # N.B. aarch64 is not officially supported (yet), but seems to be working (for OF3-used primitives at least)
+  platforms = ["linux-64", "linux-aarch64"]
+
+  # aarch64 is not built in CF, so at the moment installing from sdist and crossing fingers
+  [feature.deepspeed.target.linux-64.dependencies]
+  deepspeed = ">=0.18.7"
+  [feature.deepspeed.target.linux-aarch64.pypi-dependencies]
+  deepspeed = ">=0.18.7"
+
+  [feature.deepspeed-build.dependencies]
+  # These are only needed to build local extensions the first time
+  # Think on whether we want to delete them afterward and how it would play with the user
+  ninja = "*"
+  cutlass = "*"
+  cuda-minimal-build = "*"
+  libcusparse-dev = "*"
+  libcublas-dev = "*"
+  libcusolver-dev = "*"
+  libcurand-dev = "*"
+
+  [feature.deepspeed-build.activation]
+  # Trick deepspeed - we could also point to $CONDA_PREFIX
+  env.CUTLASS_PATH = "DS_IGNORE_CUTLASS_DETECTION"
+  # --- Isolating completely the environment, including built extensions
+  # Note that this might not play well with advanced users or people who do not want to recompile
+  # So we likely do not want to enforce it or document it well
+
+  # Change triton cache to be isolated
+  env.TRITON_CACHE_DIR = "$CONDA_PREFIX/caches/triton"
+  # Change torch extensions cache, used by deepspeed, to be isolated
+  env.TORCH_EXTENSIONS_DIR = "$CONDA_PREFIX/caches/torch_extensions"
+
+
+# --- CuEquivariance
+# https://developer.nvidia.com/cuequivariance#section-get-started
+#
+# Problems (2026/01/13)
+# --------------------
+# 1) Missing conda packages for cuequivariance kernels
+#    In CF we have cuequivariance and cuequivariance-torch
+#    At the moment the optimized kernels are not distributed in conda-forge
+#     * cuequivariance-ops-torch-cu12
+#   There are no sources and LICENSE does not allow to redistribute wheels, so not very CF friednly.
+#   This install some other libs from pypi:
+#     * cuequivarance-ops-cu12
+#     * nvidia-cublas-cu12
+#   With cublas being the problematic one - also packaged in CF but not clobbering
+#   We would need to also package this in conda-forge
+#   See also: https://github.com/NVIDIA/cuEquivariance/issues/218
+#
+# 2) Tests fail with cuequivariance >=0.8, need to assess + pinning in the meantime
+# 2.1) No aarch wheel for cuequivariance-ops-torch-cu13 <0.8
+#
+
+[feature.cuequivariance-cuda12.target.linux-64.pypi-dependencies]
+cuequivariance = "<0.8"
+cuequivariance-torch = "<0.8"
+cuequivariance-ops-torch-cu12 = "<0.8"
+
+[feature.cuequivariance-cuda13.target.linux-64.pypi-dependencies]
+cuequivariance = "<0.8"
+cuequivariance-torch = "<0.8"
+cuequivariance-ops-torch-cu13 = "<0.8"
+
+# --- Tasks
+
+[feature.pixi-to-conda-lock.pypi-dependencies]
+pixi-to-conda-lock = ">=0.4.3"
+# we were hitting a bug for all environments that bring pytorch from pytorch indices
+# see https://github.com/basnijholt/pixi-to-conda-lock/pull/12
+
+
+[tasks]
+
+export-conda.args = [
+    { "arg" = "environment", "default" = "openfold3-cpu" },
+    { "arg" = "platform", "default" = "linux-64" },
+]
+export-conda.cmd = [
+    "echo",
+    "# Pixi generated this environment, please do not edit manually.",
+    ">$PIXI_PROJECT_ROOT/environments/{{ environment }}_{{ platform }}.yml",
+    "&&",
+    "pixi",
+    "workspace",
+    "export",
+    "conda-environment",
+    "--environment",
+    "{{ environment }}",
+    "--platform",
+    "{{ platform }}",
+    ">>$PIXI_PROJECT_ROOT/environments/{{ environment }}_{{ platform }}.yml",
+]
+
+export-conda-all.depends-on = [
+    { task = "export-conda", args = [ { environment = "openfold3-cpu" }, { platform = "linux-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cpu" }, { platform = "linux-aarch64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cpu" }, { platform = "osx-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cpu" }, { platform = "osx-arm64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12" }, { platform = "linux-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12" }, { platform = "linux-aarch64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12" }, { platform = "osx-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12" }, { platform = "osx-arm64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12-pypi" }, { platform = "linux-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12-pypi" }, { platform = "linux-aarch64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12-pypi" }, { platform = "osx-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda12-pypi" }, { platform = "osx-arm64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13" }, { platform = "linux-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13" }, { platform = "linux-aarch64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13" }, { platform = "osx-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13" }, { platform = "osx-arm64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13-pypi" }, { platform = "linux-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13-pypi" }, { platform = "linux-aarch64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13-pypi" }, { platform = "osx-64" } ]},
+    { task = "export-conda", args = [ { environment = "openfold3-cuda13-pypi" }, { platform = "osx-arm64" } ]},
+]
+
+export-conda-lock.args = [
+    { "arg" = "environment", "default" = "openfold3-cpu" },
+]
+export-conda-lock.cmd = [
+    "pixi-to-conda-lock",
+    "$PIXI_PROJECT_ROOT/pixi.lock",
+    "--output",
+    "$PIXI_PROJECT_ROOT/environments",
+    "--environment",
+    "{{ environment }}"
+    # For this one I feel we need pixi.lock to contain variables and pixi-to-conda-lock to support
+    # (or maybe for pixi-to-conda-lock to read from pixi.toml instead)
+]
+
+export-conda-lock-all.depends-on = [
+    { task = "export-conda-lock", args = [ { environment = "openfold3-cpu" } ]},
+    { task = "export-conda-lock", args = [ { environment = "openfold3-cuda12" } ]},
+    { task = "export-conda-lock", args = [ { environment = "openfold3-cuda12-pypi" } ]},
+    { task = "export-conda-lock", args = [ { environment = "openfold3-cuda13" } ]},
+    { task = "export-conda-lock", args = [ { environment = "openfold3-cuda13-pypi" } ]},
+]
+
+
+# Running a task on an environment will not work unless the task is defined in one of its features.
+# See: https://github.com/prefix-dev/pixi/issues/5380
+[feature.tests]
+tasks.test.cmd = [
+    "mkdir",
+    "-p",
+    "$PIXI_PROJECT_ROOT/test-results/{{ pixi.environment.name }}_{{ pixi.platform }}",
+    "&&",
+    "python",
+    "-m",
+    "pytest",
+    "-v",
+    ".",
+    "&>$PIXI_PROJECT_ROOT/test-results/{{ pixi.environment.name }}_{{ pixi.platform }}/tests_{{ pixi.environment.name }}_{{ pixi.platform }}.log"
+]
+
+# This workspace is massive and pushes makes pixi push the limits of the system
+# This is an example update command which should work regardless of user OSX setup
+tasks.safe-but-slow-update.cmd = [
+    "pixi",
+    "update",
+    # This and --tls-no-verify can help with SSL struggles in corporate environments
+    "--tls-root-certs",
+    "all",
+    # These can help avoiding running out of system resources (e.g., file handles in osx, greedy pixi...)
+    "--concurrent-downloads",
+    "20",
+    "--concurrent-solves",
+    "4"
+]
diff --git a/pyproject.toml b/pyproject.toml
index 6837874bd..5a5d4c690 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,103 +6,106 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "openfold3"
 version = "0.4.0"
-dependencies = [
-  "awscli",
-  "awscrt",
-  "torch",# ==2.5.1",
-  "pytorch-lightning >=2.1",
-  "numpy",
-  "pandas",
-  "PyYAML",
-  "requests",
-  "scipy",
-  "tqdm",
-  "typing-extensions",
-  "wandb",
-  "ml-collections",
-  "mkl",
-  "aria2",
-  "biotite",
-  "rdkit",
-  "boto3",
-  "memory_profiler",
-  "func_timeout",
-  "lmdb", # == 1.6  # This verison might be required to avoid Error during training
-  "ijson",
-  "deepspeed",
-  "pdbeccdutils",
-  # For cutlass >=4, import library is cutlass_cppgen, but deepspeed is
-  # currently using cutlass.
-  "nvidia-cutlass <4",
-  "kalign-python",
-
-  # additional pins
-
-  # Pinned cutlass <4 calls from cuda.__version__, which was removed when
-  # cuda-python went fully metapackage
-  "cuda-python <12.9.1",
-]
 authors = [
-  {name = "OpenFold Team", email = "support@openfold.io" }
+    { name = "OpenFold Team", email = "support@openfold.io" }
 ]
 description = "OpenFold's Biological Structure Prediction Model based on DeepMind's AlphaFold 3"
 readme = "README.md"
-requires-python = ">=3.10"
 license = { text = "Apache-2.0" }
 classifiers = [
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
 ]
+urls.Homepage = "https://openfold.io/"
+urls.Documentation = "https://openfold-3.readthedocs.io/en/latest/"
+urls.Repository = "https://github.com/aqlaboratory/openfold-3"
+urls.Issues = "https://github.com/aqlaboratory/openfold-3/issues"
 
-[project.urls]
-Repository = "https://github.com/aqlaboratory/openfold-3"
+scripts.run_openfold = "openfold3.run_openfold:cli"
+scripts.setup_openfold = "openfold3.setup_openfold:main"
+
+requires-python = ">=3.10"
+dependencies = [
+    "numpy",
+    "scipy",
+    "pandas",
+    "torch", # ==2.5.1",
+    "ml-collections",
+    "pytorch-lightning >=2.1",
+    "biotite",
+    "rdkit",
+    "pdbeccdutils",
+    "kalign-python",
+    "requests",
+    "awscli",
+    "awscrt",
+    "boto3",
+    "PyYAML",
+    "ijson",
+    "memory_profiler",
+    "wandb",
+    "func_timeout",
+    "tqdm",
+    "typing-extensions",
+    "lmdb", # == 1.6  # This verison might be required to avoid Error during training
+]
 
-[project.scripts]
-run_openfold="openfold3.run_openfold:cli"
-setup_openfold="openfold3.setup_openfold:main"
+optional-dependencies.dev = [
+    "pytest",
+    "pytest-xdist",
+    "pytest-cov",
+    "pytest-benchmark",
+    "ruff",
+
+    # used for documentation
+    "sphinx",
+    "myst-parser",
+    "furo"
+]
+optional-dependencies.cuequivariance = [
+    "cuequivariance>=0.6.1,<0.8",
+    "cuequivariance-ops-torch-cu12>=0.6.1,<0.8",
+    "cuequivariance-torch>=0.6.1,<0.8",
+    "torch>=2.7",
+]
+optional-dependencies.deepspeed = [
+    "deepspeed>=0.18.7",
+]
 
+# Let's take a decision if these are optional-dependencies or dependency-groups
+# See: https://github.com/astral-sh/uv/issues/9011
+# Leaving here to not break ongoing docker revamp efforts
 [dependency-groups]
 test = [
-  "pytest",
-  "ruff",
-  "awscli",
-  "aria2",
-  "pytest-xdist",
-  "pytest-cov",
-  "pytest-benchmark",
-  "debugpy",
+    "pytest",
+    "ruff",
+    "awscli",
+    "aria2",
+    "pytest-xdist",
+    "pytest-cov",
+    "pytest-benchmark",
+    "debugpy",
 ]
 
-[project.optional-dependencies]
-dev = [
-  "pytest",
-  "ruff",
-  # used for documentation
-  "sphinx",
-  "myst-parser",
-  "furo"
-]
-cuequivariance = [
-  "cuequivariance>=0.6.1",
-  "cuequivariance-ops-torch-cu12>=0.6.1",
-  "cuequivariance-torch>=0.6.1",
-  "torch>=2.7",
-]
 
 [tool.setuptools]
 include-package-data = true
 
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["openfold3*", "scripts*"] 
+include = ["openfold3*", "scripts*"]
 
 [tool.setuptools.package-data]
 openfold3 = [
-  "projects/*/config/*.yml",
-  "tests/test_data/**/*",
-  "scripts/*.sh"
+    "projects/*/config/*.yml",
+    "tests/test_data/**/*",
+    "scripts/*.sh"
 ]
 
 # much of the cibuildwheel config taken from benfred/implicit