docs: use commands instead of python invocation in README

README.md

 # Perun proxy utils
 
+Scripts and monitoring probes related to Perun ProxyIdP.
+
+## Installation
+
+Install via pip:
+
+```sh
+pip install perun.proxy.utils
+```
+
+There are several extras which are required only for some scripts:
+
+- `[ldap]` for check_ldap and check_ldap_syncrepl
+  - this also requires installing [build prerequisites of the python-ldap library](https://www.python-ldap.org/en/latest/installing.html#build-prerequisites)
+- `[postgresql]` for check_pgsql
+
 ## Scripts
 
-### run_probes.py
+### run_probes
 
 - script designed to execute multiple monitoring probes
 - output is compatible with CheckMK
 - it is required to put configuration file to `/etc/run_probes_cfg.yaml`
-- for usage run: `./run_probes.py` or `python3 -m perun.proxy.utils.run_probes`
+
+For usage instructions, run:
+
+```sh
+run_probes
+```
 
 ### separate_ssp_script.py
 
@@ -52,30 +73,46 @@
 
 All nagios scripts are located under `nagios` directory.
 
-### check_mongodb.py
+### check_mongodb
+
+Nagios monitoring probe for mongodb.
+
+Tested options:
 
-- nagios monitoring probe for mongodb
+- connect
+- connections
+- replication_lag
+- replset_state
 
-- connect, connections, replication_lag, replset_state monitoring options are tested (some possible options may not work since there are constructs which are not supported by latest mongodb versions)
+(some possible options may not work since there are constructs which are not supported by the latest mongodb versions)
 
-- for usage run:
-  `python3 check_mongodb.py --help`
+For usage instructions, run:
+
+```sh
+check_mongodb --help
+```
 
 ### check_saml.py
 
-- SAML authentication check
+SAML authentication check compatible with SimpleSAMLphp and mitreID.
+
+For usage instructions, run:
 
-- for usage run:
-  `python3 check_saml.py --help`
+```sh
+check_saml --help
+```
 
 ### check_user_logins.py
 
-- check users which login in repeatedly more often than a specified threshold (logins per seconds)
+Check users which login in repeatedly more often than a specified threshold (logins per seconds).
+
+For usage instructions, run:
 
-- for usage run:
-  `python3 check_user_logins.py --help`
+```sh
+check_user_logins --help
+```
 
-- example:
+Example:
 
 ```sh
 python3 check_user_logins.py
@@ -86,63 +123,43 @@ python3 check_user_logins.py
     -d "%b %d %Y %H:%M:%S"
 ```
 
-### check_ldap.py
+### check_ldap
 
-- check whether LDAP is available
-- to use this check, you must install the ldap extra:
+Check whether an LDAP server is available.
 
-  ```sh
-  pip install perun.proxy.utils[ldap]
-  ```
+For usage instructions, run:
 
-  and the [build prerequisites of the python-ldap library](https://www.python-ldap.org/en/latest/installing.html#build-prerequisites)
-
-- for usage run:
-
-  ```sh
-  python3 check_ldap.py --help
-  ```
+```sh
+check_ldap --help
+```
 
 ### check_ldap_syncrepl
 
-- check whether an LDAP replica is up to date with the provider
-- to use this check, you must install the ldap extra:
+Check whether an LDAP replica is up to date with the provider.
 
-  ```sh
-  pip install perun.proxy.utils[ldap]
-  ```
+#### Usage
 
-  and the [build prerequisites of the python-ldap library](https://www.python-ldap.org/en/latest/installing.html#build-prerequisites)
-
-- for usage run:
-
-  ```sh
-  check_ldap_syncrepl --help
-  ```
-
-### check_privacyidea.py
+```sh
+check_ldap_syncrepl --help
+```
 
-- check whether privacyidea is available
-- use caching arguments for avoiding failure when one TOTP code is used two times
+### check_privacyidea
 
-- for usage run:
+Check whether privacyidea is available by performing TOTP authentication via the API.
+Use caching arguments for avoiding failure when one TOTP code is used two times.
 
-  ```sh
-  python3 check_privacyidea.py --help
-  ```
+For usage instructions, run:
 
-### check_pgsql.py
+```sh
+check_privacyidea --help
+```
 
-- check connection to PostgreSQL
-- possible check with configurable query
-- to use this check you must include the postgresql extra, which will install [psycopg2-binary](https://pypi.org/project/psycopg2-binary/):
+### check_pgsql
 
-  ```sh
-  pip install perun.proxy.utils[postgresql]
-  ```
+Check connection to PostgreSQL using a configurable query.
 
-- for usage run:
+For usage instructions, run:
 
-  ```sh
-  python3 check_pgpsql.py --help
-  ```
+```sh
+check_pgsql --help
+```