Commit cd5ac937 authored by Jacob Durrant's avatar Jacob Durrant

Updated text, version, etc.

parent 3a4d3e1d
Changes
=======
WIP (4.0.1)
-----------
4.0.1
-----
* Updated Gypsum-DL to version 1.1.4.
* Updated Dimorphite-DL to version 1.2.3.
* Revised
`$PATH/autogrow4/accessory_scripts/convert_vina_docked_pdbqt_to_pdbs.py` to
convert files that label atoms as `HETATM`, Previously, this script only
convert files that label atoms as `HETATM`. Previously, this script only
converted atoms that were labeled as `ATOM`.
* Revised
`$PATH/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py` to
remove `None` objects which failed to be imported into RDKit. This prevents
remove `None` objects that could not be imported into RDKit. This prevents
the `None` objects from causing errors in `def convert_single_sdf_to_pdb`.
* Add `raise Exception` in
`$PATH/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py` with
debugging instructions if Gypsum-Dl produced are no SDF files. `raise
Exception` added to `def convert_sdf_to_pdbs`.
* Add `raise Exception` in
`$PATH/autogrow4/docker/autogrow_in_docker.py` to check for `sudo` and administer
privileges.
* Add `--override_sudo_admin_privelledges` variable for
`$PATH/autogrow4/docker/autogrow_in_docker.py` skip the check for `sudo` and administer
privileges for docker-compatible OS that do not have such permissions.
* Fix dependency versions installed in `$PATH/autogrow4/docker/Dockerfile`. This
ensures that AutoGrow4 continues to run in Docker even if dependency updates
cause compatibility issues.
* Added a AutoGrow4 citation to the print statement and `$PATH/autogrow4/RunAutogrow.py`.
debugging instructions if Gypsum-DL produces no SDF files. `raise Exception`
added to `def convert_sdf_to_pdbs`.
* Add `raise Exception` in `$PATH/autogrow4/docker/autogrow_in_docker.py` to
check for `sudo` and administrator privileges.
* Add `--override_sudo_admin_privileges` parameter to
`$PATH/autogrow4/docker/autogrow_in_docker.py`. This parameter skips the
check for `sudo` and administrator privileges for docker-compatible OS that
do not have such permissions.
* Fix dependency versions installed in `$PATH/autogrow4/docker/Dockerfile`.
This ensures that AutoGrow4 continues to run in Docker even if future
dependency updates cause compatibility issues.
* Added an AutoGrow4 citation to the print statement in
`$PATH/autogrow4/RunAutogrow.py`.
* Revised `./docker/README.md` to clarify docker use.
* Updated the docker scripts. Bug fixes, added `--rm` to the docker command,
etc.
* Revised `$PATH/autogrow4/autogrow/user_vars.py` to correct minor typos with OS checks.
* Revised `$PATH/autogrow4/autogrow/user_vars.py` to correct minor typos with
OS checks.
* Updated `$PATH/autogrow4/README.md` with minor updates and developer notes.
* Added `Dependencies Notes` to `$PATH/autogrow4/README.md`.
* Added `Developer Notes` to `$PATH/autogrow4/docker/README.md`.
......
......@@ -36,25 +36,27 @@ We strongly recommend running AutoGrow4 via Docker using
## Dependencies Notes
AutoGrow4 version 4.0.1 has been tested to run using the following dependencies:
```python
>>> rdkit.__version__
'2020.03.1'
>>> numpy.__version__
'1.18.1'
>>> scipy.__version__
'1.4.1'
>>> matplotlib.__version__
'3.2.1'
>>> func_timeout.__version__
'4.3.5'
```
AutoGrow4 version 4.0.1 has been tested with the following dependencies:
If you are unable to run AutoGrow4, please try running AutoGrow4 in an environment
using these releases these dependencies, or the Docker version of AutoGrow4 which
automatically installs dependencies verified to work with AutoGrow4. If you discover
AutoGrow4 is no longer compatible with current library releases, please contact us
and we will attempt to correct the code.
```python
>>> rdkit.__version__
'2020.03.1'
>>> numpy.__version__
'1.18.1'
>>> scipy.__version__
'1.4.1'
>>> matplotlib.__version__
'3.2.1'
>>> func_timeout.__version__
'4.3.5'
```
If you are unable to run AutoGrow4, please try running AutoGrow4 in a python
environment with these specific dependencies. Alternatively, the Docker
version of AutoGrow4 automatically installs dependencies that are verified to
work with AutoGrow4. If you discover tha tAutoGrow4 is no longer compatible
with current library releases, please contact us, and we will attempt to
correct the code.
## Developer Note
......@@ -64,7 +66,8 @@ Yablonski S, Durrant JD (2019) Dimorphite-DL: An open-source program for
enumerating the ionization states of drug-like small molecules. J Cheminform
11:14. doi:10.1186/s13321-019-0336-9.
Running AutoGrow4 using Docker uses current versions of its dependencies
as of May 2020. These have been tested to be compatible with AutoGrow4. Future
development of AutoGrow4 should test the current versions of these dependencies
and update `$PATH/docker/Dockerfile` appropriately.
\ No newline at end of file
As of May 2020, AutoGrow4 works in the provided Docker container (with the
specific, hard-coded versions of the dependencies). These dependencies are
known to be compatible with AutoGrow4. When developing future versions of
AutoGrow4, be sure to test the current versions of these dependencies and to
update `$PATH/docker/Dockerfile` appropriately.
......@@ -639,13 +639,13 @@ PARSER.add_argument(
already installed in the docker image.",
)
PARSER.add_argument(
"--override_sudo_admin_privelledges",
metavar="param.override_sudo_admin_privelledges",
"--override_sudo_admin_privileges",
metavar="param.override_sudo_admin_privileges",
default=False,
help="Docker normally requires `sudo` (linux/macos) or `Administrator` \
privileges (windows/cygwin). If an system does not have such privelledges, \
or does not require such privelledges, setting this to True, will skip the \
check for privelledges. This variable is provided via commandline, and \
privileges (windows/cygwin). If an system does not have such privileges, \
or does not require such privileges, setting this to True, will skip the \
check for privileges. This variable is provided via commandline, and \
IS NOT RECOMMENDED for most OS. ",
)
ARGS_DICT = vars(PARSER.parse_args())
......@@ -655,9 +655,9 @@ print("BE SURE TO RUN THIS SCRIPT WITH SUDO (LINUX/MACOS) OR ADMINISTRATOR")
print("(WINDOWS) PRIVILEGES!")
print("")
# Check that this is running with appropriate privelledges.
# i.e., sudo (linux/macos) or Administrator privelledges (Windows/cygwin)
if ARGS_DICT["override_sudo_admin_privelledges"] == False:
# Check that this is running with appropriate privileges.
# i.e., sudo (linux/macos) or Administrator privileges (Windows/cygwin)
if ARGS_DICT["override_sudo_admin_privileges"] == False:
if sys.platform.lower() in ["darwin", "linux", "linux2"]:
if os.getuid() != 0:
printout = "\n\nMust run this script with `sudo` privileges.\n\t"
......@@ -679,8 +679,8 @@ if ARGS_DICT["override_sudo_admin_privelledges"] == False:
else:
print("\n##############################################################")
print("WARNING: Skipping check for privelledges.")
print("\tBE SURE TO RUN THIS SCRIPT WITH APPROPRIATE PRIVELLEDGES:")
print("WARNING: Skipping check for privileges.")
print("\tBE SURE TO RUN THIS SCRIPT WITH APPROPRIATE PRIVILEGES:")
print("\tSUDO (LINUX/MACOS) OR ADMINISTRATOR (WINDOWS) PRIVILEGES!")
print("\tFailure to do so may result in Docker failures.")
print("##############################################################\n")
......
......@@ -63,3 +63,4 @@ fi
exit
# For interactive/debug add bottom line
# bash
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