Merge pull request #244 from kipoi/pin-pip

Pin pip version across all model groups
kipoi · Apr 1, 2021 · c14cd96 · c14cd96
2 parents 55a03dc + 4f3d1f4
commit c14cd96
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Showing 34 changed files with 139 additions and 112 deletions.
diff --git a/BPNet-OSKN/model.yaml b/BPNet-OSKN/model.yaml
@@ -34,18 +34,18 @@ dependencies:
       - bioconda::pysam>=0.14.0
       - bioconda::genomelake==0.1.4
 
-      - pytorch::pytorch  # optional for data-loading
-      - cython
-      - h5py>=2.7.0
-      - numpy
+      - pytorch::pytorch=1.4.0  # optional for data-loading
+      - cython=0.29.22
+      - h5py=2.10.0
+      - numpy=1.19.2
 
-      - pandas>=0.23.0
-      - fastparquet
-      - python-snappy
-
-      - nb_conda
+      - pandas=1.1.5
+      - fastparquet=0.5.0
+      - python-snappy=0.6.0
+      - pip=21.0.1
+      - nb_conda=2.2.1
     pip:
-      - tensorflow>=1.0,<1.15
+      - tensorflow==1.14.0
       - git+https://github.com/kundajelab/DeepExplain.git
       - keras==2.2.4
       - git+https://github.com/kundajelab/bpnet.git@0cb7277b736260f8b4084c9b0c5bd62b9edb5266

diff --git a/CpGenie/merged/model.yaml b/CpGenie/merged/model.yaml
@@ -36,11 +36,12 @@ default_dataloader:
     dummy_axis: 1
 dependencies:
   conda:
-    - python=3.6
+    - python=3.6.12
     - h5py=2.10.0
     - tensorflow=1.10.0
     - keras=1.2.2
     - pysam=0.15.3
+    - pip=20.2.4
 schema:
   inputs:
     name: seq

diff --git a/CpGenie/model-template.yaml b/CpGenie/model-template.yaml
@@ -48,10 +48,12 @@ default_dataloader:
     dummy_axis: 1
 dependencies:
   conda:
+    - python=3.6.12
     - h5py=2.10.0
     - tensorflow=1.10.0
     - keras=1.2.2
     - pysam=0.15.3
+    - pip=20.2.4
 schema:
   inputs:
     name: seq

diff --git a/DeepBind/model-template.yaml b/DeepBind/model-template.yaml
@@ -37,11 +37,13 @@ default_dataloader:
 
 dependencies:
   conda:
+    - python=3.6.12
     - h5py=2.10.0
     - tensorflow=1.4.1
     - keras=2.1.6
     - python=3.6
     - pysam=0.15.3
+    - pip=20.2.4
 schema:
   inputs:
     name: seq

diff --git a/DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml b/DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml
@@ -12,12 +12,11 @@ args:
 defined_as: dataloader.py::SeqDataset
 dependencies:
   conda:
-  - bioconda::genomelake==0.1.4
-  - bioconda::pybedtools
-  - python=3.5
-  - numpy
-  - pandas
-  - cython
+  - bioconda::genomelake=0.1.4
+  - bioconda::pybedtools=0.8.1
+  - python=3.6
+  - numpy=1.19.2
+  - pandas=1.1.3
 info:
   authors:
   - github: avsecz

diff --git a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml
@@ -11,12 +11,12 @@ args:
 default_dataloader: .
 dependencies:
   conda:
-  - python=3.5
-  - h5py
+    - python=3.6
+    - h5py=2.10.0
+    - pip=20.2.4
   pip:
-  - tensorflow==1.4.1
-  - keras==1.2.2
-  - deepcpg==1.0.4
+    - tensorflow==1.10.0
+    - keras==1.2.2
 info:
   authors:
   - github: cangermueller

diff --git a/DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml b/DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml
@@ -12,12 +12,11 @@ args:
 defined_as: dataloader.py::SeqDataset
 dependencies:
   conda:
-  - bioconda::genomelake==0.1.4
-  - bioconda::pybedtools
-  - python=3.5
-  - numpy
-  - pandas
-  - cython
+    - bioconda::genomelake=0.1.4
+    - bioconda::pybedtools=0.8.1
+    - python=3.6
+    - numpy=1.19.2
+    - pandas=1.1.3
 info:
   authors:
   - github: avsecz

diff --git a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml
@@ -10,12 +10,12 @@ args:
 default_dataloader: .
 dependencies:
   conda:
-  - python=3.5
-  - h5py
+    - python=3.6
+    - h5py=2.10.0
+    - pip=20.2.4
   pip:
-  - tensorflow==1.4.1
-  - keras==1.2.2
-  - deepcpg==1.0.4
+    - tensorflow==1.10.0
+    - keras==1.2.2
 info:
   authors:
   - github: cangermueller

diff --git a/DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml b/DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml
@@ -12,12 +12,11 @@ args:
 defined_as: dataloader.py::SeqDataset
 dependencies:
   conda:
-  - bioconda::genomelake==0.1.4
-  - bioconda::pybedtools
-  - python=3.5
-  - numpy
-  - pandas
-  - cython
+    - bioconda::genomelake=0.1.4
+    - bioconda::pybedtools=0.8.1
+    - python=3.6
+    - numpy=1.19.2
+    - pandas=1.1.3
 info:
   authors:
   - github: avsecz

diff --git a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml
@@ -10,12 +10,12 @@ args:
 default_dataloader: .
 dependencies:
   conda:
-  - python=3.5
-  - h5py
+    - python=3.6
+    - h5py=2.10.0
+    - pip=20.2.4
   pip:
-  - tensorflow==1.4.1
-  - keras==1.2.2
-  - deepcpg==1.0.4
+    - tensorflow==1.10.0
+    - keras==1.2.2
 info:
   authors:
   - github: cangermueller

diff --git a/DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml b/DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml
@@ -12,12 +12,11 @@ args:
 defined_as: dataloader.py::SeqDataset
 dependencies:
   conda:
-  - bioconda::genomelake==0.1.4
-  - bioconda::pybedtools
-  - python=3.5
-  - numpy
-  - pandas
-  - cython
+    - bioconda::genomelake=0.1.4
+    - bioconda::pybedtools=0.8.1
+    - python=3.6
+    - numpy=1.19.2
+    - pandas=1.1.3
 info:
   authors:
   - github: avsecz

diff --git a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml
@@ -10,12 +10,12 @@ args:
 default_dataloader: .
 dependencies:
   conda:
-  - python=3.5
-  - h5py
+    - python=3.6
+    - h5py=2.10.0
+    - pip=20.2.4
   pip:
-  - tensorflow==1.4.1
-  - keras==1.2.2
-  - deepcpg==1.0.4
+    - tensorflow==1.10.0
+    - keras==1.2.2
 info:
   authors:
   - github: cangermueller

diff --git a/DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml b/DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml
@@ -12,12 +12,11 @@ args:
 defined_as: dataloader.py::SeqDataset
 dependencies:
   conda:
-  - bioconda::genomelake==0.1.4
-  - bioconda::pybedtools
-  - python=3.5
-  - numpy
-  - pandas
-  - cython
+    - bioconda::genomelake=0.1.4
+    - bioconda::pybedtools=0.8.1
+    - python=3.6
+    - numpy=1.19.2
+    - pandas=1.1.3
 info:
   authors:
   - github: avsecz

diff --git a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml
@@ -10,12 +10,12 @@ args:
 default_dataloader: .
 dependencies:
   conda:
-  - python=3.5
-  - h5py
+    - python=3.6
+    - h5py=2.10.0
+    - pip=20.2.4
   pip:
-  - tensorflow==1.4.1
-  - keras==1.2.2
-  - deepcpg==1.0.4
+    - tensorflow==1.10.0
+    - keras==1.2.2
 info:
   authors:
   - github: cangermueller

diff --git a/DeepCpG_DNA/template/dataloader.yaml b/DeepCpG_DNA/template/dataloader.yaml
@@ -16,12 +16,11 @@ info:
   doc: Dataloader for the DeepCpG.
 dependencies:
   conda:
-    - bioconda::genomelake==0.1.4
-    - bioconda::pybedtools
-    - python=3.5
-    - numpy
-    - pandas
-    - cython
+    - bioconda::genomelake=0.1.4
+    - bioconda::pybedtools=0.8.1
+    - python=3.6
+    - numpy=1.19.2
+    - pandas=1.1.3
 output_schema:
   inputs:
     dna:

diff --git a/DeepCpG_DNA/template/dataloader_m_template.yaml b/DeepCpG_DNA/template/dataloader_m_template.yaml
@@ -21,14 +21,11 @@ info:
   doc: Dataloader + target output for the DeepCpG model.
 dependencies:
   conda:
-    - bioconda::genomelake==0.1.4
-    - bioconda::pybedtools
-    - python=3.5
-    - numpy
-    - pandas
-  pip:
-    - cython
-    - deepcpg==1.0.4
+    - bioconda::genomelake=0.1.4
+    - bioconda::pybedtools=0.8.1
+    - python=3.6
+    - numpy=1.19.2
+    - pandas=1.1.3
 output_schema:
   inputs:
     dna:

diff --git a/DeepCpG_DNA/template/model_template.yaml b/DeepCpG_DNA/template/model_template.yaml
@@ -23,12 +23,12 @@ info:
 default_dataloader: .
 dependencies:
   conda:
-    - python=3.5
-    - h5py
+    - python=3.6
+    - h5py=2.10.0
+    - pip=20.2.4
   pip:
-    - tensorflow==1.4.1
+    - tensorflow==1.10.0
     - keras==1.2.2
-    - deepcpg==1.0.4
 schema:
   inputs:
     dna:

diff --git a/DeepSEA/beluga/model.yaml b/DeepSEA/beluga/model.yaml
@@ -32,8 +32,10 @@ default_dataloader:
 
 dependencies:
   conda:
-    - h5py
-    - pytorch::pytorch-cpu>=1.0.0
+    - python=3.6.12
+    - pip=20.2.4
+    - h5py=2.10.0
+    - pytorch::pytorch-cpu=1.3.1
   pip:
     - kipoiseq
 

diff --git a/DeepSEA/predict/model.yaml b/DeepSEA/predict/model.yaml
@@ -45,8 +45,10 @@ default_dataloader:
     dtype: np.float32
 dependencies:
   conda:
-    - h5py
-    - pytorch::pytorch-cpu>=0.2.0
+    - python=3.6.12
+    - h5py=2.10.0
+    - pytorch::pytorch-cpu=1.3.1
+    - pip=20.2.4
   pip:
     - kipoiseq
 schema:

diff --git a/DeepSEA/variantEffects/model.yaml b/DeepSEA/variantEffects/model.yaml
@@ -44,8 +44,10 @@ default_dataloader:
     dtype: np.float32
 dependencies:
   conda:
-    - h5py
-    - pytorch::pytorch-cpu>=0.2.0
+    - python=3.6.12
+    - h5py=2.10.0
+    - pytorch::pytorch-cpu=1.3.1
+    - pip=20.2.4
   pip:
     - kipoiseq
 schema:

diff --git a/Framepool/model.yaml b/Framepool/model.yaml
@@ -13,6 +13,7 @@ dependencies:
     - tensorflow=1.13.1
     - keras=2.2.4
     - h5py=2.9.0
+    - pip=20.2.4
   pip:
     - kipoi
 

diff --git a/HAL/model.yaml b/HAL/model.yaml
@@ -8,6 +8,7 @@ dependencies:
   conda:
     - numpy=1.19.2
     - python=3.6
+    - pip=20.2.4
   pip:
     - arrow==0.17.0
     - attrs==20.2.0

diff --git a/MMSplice/deltaLogitPSI/model.yaml b/MMSplice/deltaLogitPSI/model.yaml
@@ -14,6 +14,9 @@ info:
     tags:
         - RNA splicing
 dependencies:
+    conda:
+      - python=3.6.13
+      - pip=21.0.1
     pip:
       - h5py==2.10.0
       - mmsplice==1.0.3

diff --git a/MMSplice/modularPredictions/model.yaml b/MMSplice/modularPredictions/model.yaml
@@ -14,9 +14,12 @@ info:
     tags:
         - RNA splicing
 dependencies:
-    pip:
-      - h5py==2.10.0
-      - mmsplice==1.0.3
+  conda:
+    - python=3.6.13
+    - pip=21.0.1
+  pip:
+    - h5py==2.10.0
+    - mmsplice==1.0.3
 schema:
     inputs:
       seq:

diff --git a/MMSplice/mtsplice/model.yaml b/MMSplice/mtsplice/model.yaml
@@ -14,6 +14,9 @@ info:
     tags:
         - RNA splicing
 dependencies:
+    conda:
+    - python=3.6.13
+    - pip=21.0.1
     pip:
       - h5py==2.10.0
       - mmsplice==2.0.0