Merge pull request #180 from EGA-archive/EE-2619_pypi-docs

EE-2619 Update PyPI description

README.md

@@ -17,25 +17,6 @@ The pyEGA3 download client is a python-based tool for viewing and downloading fi
 
 * Python 3.6 or newer. ([download instructions](https://www.python.org/downloads/))
 
-### Firewall ports
-
-pyEGA3 makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443) and the EGA Data API (https://ega.ebi.ac.uk:8052). Ports 8443 and 8052 must both be reachable from the location where pyEGA3 is executed to avoid timeouts.
-
-For Linux/Mac users, check if ports 8443 and 8052 are open by running the following commands:
-
-```bash
-openssl s_client -connect ega.ebi.ac.uk:8443
-openssl s_client -connect ega.ebi.ac.uk:8052
-```
-
-If the ports are open, the commands should print `CONNECTED` to the terminal.
-
-For Windows users, check if ports 8443 and 8052 are open by going to the following URLs:
-* https://ega.ebi.ac.uk:8443/ega-openid-connect-server/
-* https://ega.ebi.ac.uk:8052/elixir/central/stats/load
-
-If the ports are open, both of the sites should load with no timeouts.
-
 ## Installation and update
 
 ### Using Pip3
@@ -234,7 +215,7 @@ pyega3 -c 5 -cf </Path/To/CREDENTIALS_FILE> fetch EGAD<NUM> --output-dir </Path/
 ```bash
 usage: pyega3 fetch [-h] [--reference-name REFERENCE_NAME]
                     [--reference-md5 REFERENCE_MD5] [--start START]
-                    [--end END] [--format {BAM,CRAM}]
+                    [--end END] [--format {BAM,CRAM,VCF,BCF}]
                     [--max-retries MAX_RETRIES] [--retry-wait RETRY_WAIT]
                     [--output-dir OUTPUT_DIR] [--delete-temp-files]
                     identifier
@@ -260,7 +241,7 @@ optional arguments:
   --end END, -e END     The end position of the range on the reference,
                         0-based exclusive. If specified, reference-name or
                         reference-md5 must also be specified.
-  --format {BAM,CRAM}, -f {BAM,CRAM}
+  --format {BAM,CRAM,VCF,BCF}, -f {BAM,CRAM,VCF,BCF}
                         The format of data to request.
   --max-retries MAX_RETRIES, -M MAX_RETRIES
                         The maximum number of times to retry a failed

setup.py

@@ -31,7 +31,7 @@
     name="pyega3",
     description="EGA python client",
     long_description=long_description,
-    long_description_content_type="text/plain",
+    long_description_content_type="text/markdown",
     packages=find_packages(),
     version=VERSION,
     author="EGA team",