diff --git a/.github/workflows/ingestion-ci.yml b/.github/workflows/ingestion-ci.yml
index 891c6ff5..03df48d9 100644
--- a/.github/workflows/ingestion-ci.yml
+++ b/.github/workflows/ingestion-ci.yml
@@ -21,9 +21,11 @@ jobs:
         python-version: ["3.9"]
 
     steps:
-      # - uses: actions/checkout@v4
-      - name: Download Conda YAML file
-        run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/kra-gha/pipeline_env.yaml
+      - uses: actions/checkout@v4
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree
       
       - uses: conda-incubator/setup-miniconda@v3
         with:
@@ -33,8 +35,14 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: pipeline_env
-          environment-file: pipeline_env.yaml # consider moving to etc/pipeline_env.yaml
+          environment-file: pipeline_env.yaml
 
+      - name: Install Panpipes
+        shell: bash -el {0}
+        run: |
+          pip install -e .
+          conda list
+          
       - name: Conda info
         if: env.debug == 'true'
         shell: bash -el {0}
@@ -45,11 +53,6 @@ jobs:
         shell: pwsh
         run: conda list
 
-      #- name: Run tests
-      #  shell: bash -el {0}
-      #  run: |
-      #    python -m pytest tests/
-
       # Note: all three files are renamed during the download to trim the "subsample_" prefix
       - name: Preparing the data
         run: |
@@ -89,7 +92,7 @@ jobs:
 
       - name: File tree
         if: env.debug == 'true'
-        run: tree
+        run: tree teaseq
 
       - name: Review pipeline tasks
         shell: bash -el {0}
@@ -105,4 +108,10 @@ jobs:
         
       - name: File tree
         if: env.debug == 'true'
-        run: tree
+        run: tree teaseq
+        
+      - uses: actions/upload-artifact@v4
+        with:
+          name: teaseq_unfilt.h5mu
+          path: teaseq/ingest/teaseq_unfilt.h5mu
+          retention-days: 1
diff --git a/pipeline_env.yaml b/pipeline_env.yaml
index 0b765992..b0e11027 100644
--- a/pipeline_env.yaml
+++ b/pipeline_env.yaml
@@ -14,5 +14,4 @@ dependencies:
   - r-xtable
   - pip
   - pip:
-    - panpipes[spatial]
     - pytest
diff --git a/pyproject.toml b/pyproject.toml
index a9c55b95..e539d40b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,14 +35,16 @@ dependencies = [
     "cgatcore", 
     "drmaa", 
     "gevent",
-    "harmonypy", 
+    "harmonypy",
+    "jax<=0.4.23",
+    "jaxlib<=0.4.23",
     "leidenalg", 
     "louvain",
     "matplotlib<=3.7.3",
     "mofapy2",
     "mudata>=0.2.1",
     "muon",
-    "numpy>=1.22.4", 
+    "numpy==1.22.4", 
     "openpyxl",
     "packaging", 
     "pandas>=1.0", 
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 34619535..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,232 +0,0 @@
-absl-py==1.3.0
-adjustText==0.7.3
-aiohttp==3.8.3
-aiosignal==1.2.0
-airr==1.4.1
-anndata==0.8.0
-annoy==1.17.1
-anyio==3.6.2
-apsw==3.39.4.0
-argon2-cffi==21.3.0
-argon2-cffi-bindings==21.2.0
-asttokens==2.0.8
-async-timeout==4.0.2
-attrs==22.1.0
-Babel==2.11.0
-backcall==0.2.0
-bbknn==1.5.1
-bcrypt==4.0.1
-beautifulsoup4==4.11.1
-bleach==5.0.1
-Bottleneck @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/Bottleneck/Bottleneck-1.3.2
-cached-property==1.5.2
-cachetools==5.2.0
-certifi==2022.9.24
-cffi==1.15.1
-cgatcore==0.6.14
-charset-normalizer==2.1.1
-chex==0.1.5
-commonmark==0.9.1
-contextlib2==21.6.0
-contourpy==1.0.5
-cryptography==38.0.1
-cycler==0.11.0
-Cython==0.29.32
-deap @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/deap/deap-1.3.1
-debugpy==1.6.3
-decorator==5.1.1
-defusedxml==0.7.1
-dm-tree==0.1.7
-docrep==0.3.2
-drmaa==0.7.9
-entrypoints==0.4
-et-xmlfile==1.1.0
-etils==0.8.0
-exceptiongroup==1.0.0
-executing==1.1.1
-fastjsonschema==2.16.2
-fbpca==1.0
-flax==0.6.1
-fonttools==4.38.0
-frozenlist==1.3.1
-fsspec==2022.10.0
-GDAL==3.3.0
-geosketch==1.2
-gevent==22.10.1
-google-auth==2.13.0
-google-auth-oauthlib==0.4.6
-greenlet==1.1.3.post0
-grpcio==1.50.0
-h5py==3.7.0
-harmonypy==0.0.6
-idna==3.4
-igraph==0.10.2
-imageio==2.22.2
-importlib-metadata==5.0.0
-importlib-resources==5.10.0
-iniconfig==1.1.1
-intervaltree==3.1.0
-ipykernel==6.16.2
-ipython==8.5.0
-ipython-genutils==0.2.0
-ipywidgets==8.0.2
-jax==0.3.23
-jaxlib==0.3.22
-jedi==0.18.1
-Jinja2==3.1.2
-joblib==1.2.0
-json5==0.9.10
-jsonschema==4.17.0
-jupyter-server==1.21.0
-jupyter_client==7.4.4
-jupyter_core==4.11.2
-jupyterlab==3.5.0
-jupyterlab-pygments==0.2.2
-jupyterlab-widgets==3.0.3
-jupyterlab_server==2.16.2
-kiwisolver==1.4.4
-lazy_loader==0.1
-leidenalg==0.9.0
-Levenshtein==0.20.7
-lightning-utilities==0.7.1
-llvmlite==0.39.1
-louvain==0.8.0
-Markdown==3.4.1
-markdown-it-py==2.2.0
-MarkupSafe==2.1.1
-matplotlib==3.6.0
-matplotlib-inline==0.1.6
-mdurl==0.1.2
-mistune==2.0.4
-ml-collections==0.1.1
-mofapy2==0.6.7
-mpi4py @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/mpi4py/mpi4py-3.0.3
-mpmath @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/mpmath/mpmath-1.2.1
-msgpack==1.0.4
-mudata @ git+https://github.com/scverse/mudata@da2de81261db76368da0a712cf819df3abb53fb7
-multidict==6.0.2
-multipledispatch==0.6.0
-muon @ git+https://github.com/scverse/muon@8378af444f3635f095df1deee02b19e9252a61b9
-natsort==8.2.0
-nbclassic==0.4.8
-nbclient==0.7.0
-nbconvert==7.2.3
-nbformat==5.7.0
-nest-asyncio==1.5.6
-networkx==2.8.7
-notebook==6.5.2
-notebook_shim==0.2.2
-numba==0.56.3
-numexpr @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/numexpr/numexpr-2.7.3
-numpy @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/numpy/numpy-1.20.3
-numpyro==0.10.1
-nvidia-cublas-cu11==11.10.3.66
-nvidia-cuda-nvrtc-cu11==11.7.99
-nvidia-cuda-runtime-cu11==11.7.99
-nvidia-cudnn-cu11==8.5.0.96
-oauthlib==3.2.2
-openpyxl==3.0.10
-opt-einsum==3.3.0
-optax==0.1.3
-orbax==0.1.3
-packaging==21.3
-pandas @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/pandas/pandas-1.2.4
-pandocfilters==1.5.0
--e git+ssh://git@github.com/crichgriffin/panpipes_dev.git@75b32b5435efbb15ad7c66d271110ba1c1228693#egg=panpipes
-paramiko==2.11.0
-parasail==1.3.3
-parso==0.8.3
-patsy==0.5.3
-pep8==1.7.1
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow==9.2.0
-plotly==5.11.0
-pluggy==1.0.0
-prometheus-client==0.15.0
-prompt-toolkit==3.0.31
-protobuf==3.19.6
-psutil==5.9.3
-ptyprocess==0.7.0
-pure-eval==0.2.2
-pyasn1==0.4.8
-pyasn1-modules==0.2.8
-pybind11 @ file:///dev/shm/pybind11/2.6.2/GCCcore-10.3.0/pybind11-2.6.2
-pycparser==2.21
-pyDeprecate==0.3.2
-Pygments==2.13.0
-PyNaCl==1.5.0
-pynndescent==0.5.7
-pyparsing==3.0.9
-pyro-api==0.1.2
-pyro-ppl==1.8.2
-pyrsistent==0.19.2
-pysam==0.20.0
-pytest==7.2.0
-python-dateutil==2.8.2
-python-igraph==0.10.2
-python-Levenshtein==0.20.7
-pytoml==0.1.21
-pytorch-lightning==1.7.7
-pytz==2022.5
-PyWavelets==1.4.1
-PyYAML==6.0
-pyzmq==24.0.1
-rapidfuzz==2.12.0
-requests==2.28.1
-requests-oauthlib==1.3.1
-rich==12.6.0
-rsa==4.9
-ruffus==2.8.4
-scanorama==1.7.2
-scanpy==1.9.1
-scikit-image==0.19.3
-scikit-learn==1.1.3
-scikit-misc==0.1.4
-scipy @ file:///dev/shm/SciPybundle/2021.05/foss-2021a/scipy/scipy-1.6.3
-scirpy @ git+https://github.com/scverse/scirpy@02955d72382ca9371e40bc1f94d4c44046f7ca35
-scrublet==0.2.3
-scvi-tools==0.18.0
-seaborn==0.12.1
-Send2Trash==1.8.0
-session-info==1.0.0
-setuptools-scm==7.0.5
-six==1.16.0
-sniffio==1.3.0
-sortedcontainers==2.4.0
-soupsieve==2.3.2.post1
-SQLAlchemy==1.4.42
-squarify==0.4.3
-stack-data==0.5.1
-statsmodels==0.13.2
-stdlib-list==0.8.0
-tenacity==8.1.0
-tensorboard==2.10.1
-tensorboard-data-server==0.6.1
-tensorboard-plugin-wit==1.8.1
-tensorstore==0.1.33
-terminado==0.17.0
-texttable==1.6.4
-threadpoolctl==3.1.0
-tifffile==2022.10.10
-tinycss2==1.2.1
-tomli==2.0.1
-toolz==0.12.0
-torch==1.12.1
-torchmetrics==0.10.1
-tornado==6.2
-tqdm==4.64.1
-traitlets==5.5.0
-typing_extensions==4.4.0
-umap-learn==0.5.3
-urllib3==1.26.12
-wcwidth==0.2.5
-webencodings==0.5.1
-websocket-client==1.4.2
-Werkzeug==2.2.2
-widgetsnbextension==4.0.3
-yamlordereddictloader==0.4.0
-yarl==1.8.1
-zipp==3.10.0
-zope.event==4.5.0
-zope.interface==5.5.0