From 3cec3608142f18fd2d7c847b43122d5166a8d2b4 Mon Sep 17 00:00:00 2001
From: Matt Ruffalo <mruffalo@cs.cmu.edu>
Date: Thu, 14 May 2020 15:02:40 -0400
Subject: [PATCH] Update h5ad-to-arrow dependencies (#27)

* h5ad_to_arrow: bump anndata to 0.7.1, h5ad to 2.10.0

Properly fixes this:

"""
Traceback (most recent call last):
  File "/main.py", line 67, in <module>
    main(args.input_dir, args.output_dir)
  File "/main.py", line 50, in main
    h5ad_to_arrow(input_path, arrow_path)
  File "/main.py", line 13, in h5ad_to_arrow
    ann_data = read_h5ad(h5ad_file)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad
    constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 486, in _read_args_from_h5ad
    _read_key_value_from_h5(f, d, key, chunk_size=chunk_size)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 510, in _read_key_value_from_h5
    _read_key_value_from_h5(f, d[key_write], key + '/' + k, k, chunk_size)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 510, in _read_key_value_from_h5
    _read_key_value_from_h5(f, d[key_write], key + '/' + k, k, chunk_size)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 544, in _read_key_value_from_h5
    key, value = postprocess_reading(key, value)
  File "/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 541, in postprocess_reading
    value = value.astype(new_dtype)
ValueError: invalid shape in fixed-type tuple.
"""

* Ignore .idea/ (PyCharm project directory)

* h5ad-to-arrow.cwl: bump container version to new 0.0.2

In a conversation with Ilan just now, he said that I should tag and push a
new container with updated dependencies. As a bonus, this will hopefully
cause the Travis build to succeed now that the dependencies match what's in
`requirements-freeze.txt`.

* h5ad-to-arrow/.../requirements-freeze.txt: Add new auto-pulled packages
---
 .gitignore                                               | 3 +++
 containers/h5ad-to-arrow/context/requirements-freeze.txt | 8 ++++++--
 containers/h5ad-to-arrow/context/requirements.txt        | 4 ++--
 h5ad-to-arrow.cwl                                        | 2 +-
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 45ddc9a..2e2df19 100644
--- a/.gitignore
+++ b/.gitignore
@@ -132,3 +132,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# PyCharm project directory
+.idea/
diff --git a/containers/h5ad-to-arrow/context/requirements-freeze.txt b/containers/h5ad-to-arrow/context/requirements-freeze.txt
index 8318241..a54351d 100644
--- a/containers/h5ad-to-arrow/context/requirements-freeze.txt
+++ b/containers/h5ad-to-arrow/context/requirements-freeze.txt
@@ -1,4 +1,4 @@
-anndata==0.6.22.post1
+anndata==0.7.1
 asn1crypto==1.0.1
 certifi==2019.11.28
 cffi==1.12.3
@@ -6,15 +6,18 @@ chardet==3.0.4
 conda==4.7.12
 conda-package-handling==1.6.0
 cryptography==2.7
-h5py==2.9.0
+h5py==2.10.0
 idna==2.8
+importlib-metadata==1.6.0
 natsort==6.2.0
 numpy==1.17.4
+packaging==20.3
 pandas==0.25.3
 pyarrow==0.15.1
 pycosat==0.6.3
 pycparser==2.19
 pyOpenSSL==19.0.0
+pyparsing==2.4.7
 PySocks==1.7.1
 python-dateutil==2.8.1
 pytz==2019.3
@@ -24,3 +27,4 @@ scipy==1.3.3
 six==1.13.0
 tqdm==4.36.1
 urllib3==1.24.2
+zipp==3.1.0
diff --git a/containers/h5ad-to-arrow/context/requirements.txt b/containers/h5ad-to-arrow/context/requirements.txt
index 84771aa..6f9ac71 100644
--- a/containers/h5ad-to-arrow/context/requirements.txt
+++ b/containers/h5ad-to-arrow/context/requirements.txt
@@ -1,3 +1,3 @@
-anndata==0.6.22.post1
+anndata==0.7.1
 pyarrow==0.15.1
-h5py==2.9.0 # anndata fails on some inputs: https://github.com/hubmapconsortium/portal-containers/issues/1
+h5py==2.10.0
diff --git a/h5ad-to-arrow.cwl b/h5ad-to-arrow.cwl
index 993bac2..3c6702a 100755
--- a/h5ad-to-arrow.cwl
+++ b/h5ad-to-arrow.cwl
@@ -6,7 +6,7 @@ class: CommandLineTool
 baseCommand: ['python', '/main.py', '--output_dir', '.', '--input_dir']
 hints:
   DockerRequirement:
-    dockerPull: hubmap/portal-container-h5ad-to-arrow:0.0.1
+    dockerPull: hubmap/portal-container-h5ad-to-arrow:0.0.2
 inputs:
   input_directory:
     type: Directory