New noodles release

[BvB93]

Back in h5py 3.0 the default h5py.File mode was changed from "Read/write if exists, create otherwise" to "Readonly, file must exist" and while PR https://github.com/NLeSC/noodles/pull/83 was introduced to address these upstream changes, it has yet to be included in any new noodles release.

With this in mind I'd very much like to up the minimum noodles version for qmflows, as h5py-related FileNotFoundErrors are starting to pop up on a semi-regular basis.

Example traceback

``` python Exception in thread Thread-1 (patch): Traceback (most recent call last): File “/home/v13/miniconda3/envs/CAT/lib/python3.10/threading.py”, line 1009, in _bootstrap_inner self.run() File “/home/v13/miniconda3/envs/CAT/lib/python3.10/threading.py”, line 946, in run self._target(*self._args, **self._kwargs) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/thread_pool.py”, line 21, in modified_target return_value = target(*args, **kwargs) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/streams.py”, line 271, in patch for v in source(): File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/streams.py”, line 117, in map yield from map(self.f, source()) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/run/threading/sqlite3.py”, line 36, in pass_job_stream status, retrieved_result = db.add_job_to_db(key, job) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/prov/sqlite.py”, line 247, in add_job_to_db job_msg = self.registry.deep_encode(job) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/serial/registry.py”, line 231, in deep_encode return deep_map(lambda o: self.encode(o, host), obj) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in deep_map return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in deep_map return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 106, in deep_map return [deep_map(f, v) for v in result] File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 106, in return [deep_map(f, v) for v in result] File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in deep_map return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 106, in deep_map return [deep_map(f, v) for v in result] File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 106, in return [deep_map(f, v) for v in result] File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in deep_map return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in deep_map return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in deep_map return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 103, in return {k: deep_map(f, v) for k, v in result.items()} File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 106, in deep_map return [deep_map(f, v) for v in result] File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 106, in return [deep_map(f, v) for v in result] File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/lib/utility.py”, line 100, in deep_map result = f(root) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/serial/registry.py”, line 231, in return deep_map(lambda o: self.encode(o, host), obj) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/serial/registry.py”, line 187, in encode result = enc.encode(obj, make_rec) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/noodles/serial/numpy.py”, line 83, in encode f = h5py.File(self.filename) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/h5py/_hl/files.py”, line 507, in __init__ fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr) File “/home/v13/miniconda3/envs/CAT/lib/python3.10/site-packages/h5py/_hl/files.py”, line 220, in make_fid fid = h5f.open(name, flags, fapl=fapl) File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper File “h5py/h5f.pyx”, line 106, in h5py.h5f.open FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = ‘cache.hdf5’, errno = 2, error message = ‘No such file or directory’, flags = 0, o_flags = 0) ```

[jhidding]

Ok, it's been a while since I tinkered with Noodles. I created a new release and its on PyPI. Please let me know if this solves your issue.

[BvB93]

Thanks @jhidding, the update seems to have done the trick.