Add a simple cirro entrypoint (#86)

Author: sminot

.github/workflows/package.yml

@@ -33,7 +33,7 @@ jobs:
       - name: Test install
         run: |
           poetry install --all-extras
-          poetry run cirro-cli
+          poetry run cirro
 
       - name: Build python package
         run: |

README.md

@@ -26,7 +26,7 @@ If you need to change your credentials after this point, and you've opted to sav
 
 #### Downloading a dataset:
 ```bash
-Usage: cirro-cli download [OPTIONS]
+Usage: cirro download [OPTIONS]
 
   Download dataset files
 
@@ -40,7 +40,7 @@ Options:
 
 #### Uploading a dataset:
 ```bash
-Usage: cirro-cli upload [OPTIONS]
+Usage: cirro upload [OPTIONS]
 
   Upload and create a dataset
 
@@ -56,7 +56,7 @@ Options:
 
 #### Listing datasets:
 ```bash
-Usage: cirro-cli list-datasets [OPTIONS]
+Usage: cirro list-datasets [OPTIONS]
 
   List available datasets
 
@@ -73,7 +73,7 @@ When running a command, you can specify the `--interactive` flag to gather the c
 Example:
 
 ```bash
-$ cirro-cli upload --interactive
+$ cirro upload --interactive
 ? What project is this dataset associated with?  Test project
 ? Enter the full path of the data directory  /shared/biodata/test
 ? Please confirm that you wish to upload 20 files (0.630 GB)  Yes
@@ -112,7 +112,7 @@ See the following set of Jupyter notebooks that contain examples on the followin
 
 ### Configuration
 
-The `cirro-cli configure` command creates a file in `PW_HOME` called `config.ini`.
+The `cirro configure` command creates a file in `PW_HOME` called `config.ini`.
 
 You can set the `base_url` property in the config file rather than using the environment variable. 
 
@@ -135,4 +135,4 @@ enable_additional_checksums = true
 ### Clearing saved login
 
 You can clear your saved login information by removing the `~/.cirro/token.dat` file from your system or
-by running `cirro-cli configure` and selecting **No** when it asks if you'd like to save your login information.
+by running `cirro configure` and selecting **No** when it asks if you'd like to save your login information.

pyproject.toml

@@ -31,6 +31,7 @@ flake8 = "*"
 
 [tool.poetry.scripts]
 cirro-cli = "cirro.cli.cli:main"
+cirro = "cirro.cli.cli:main"
 
 [build-system]
 requires = ["poetry-core"]

samples/Using-R.ipynb

@@ -11,14 +11,18 @@
     "  \n",
     " 2. Install the reticulate package in R (with `install.packages(\"reticulate\")` from the R prompt)\n",
     "  \n",
-    " 3. Log in to your Data Portal account (with `cirro-cli configure` from the command line)\n"
+    " 3. Log in to your Data Portal account (with `cirro configure` from the command line)\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 1,
    "id": "411cdb7c",
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# Once your system is set up, you can use reticulate to import the client library\n",
@@ -30,7 +34,11 @@
    "cell_type": "code",
    "execution_count": 2,
    "id": "98697188",
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# As described in the Getting Started notebook, the `portal` object is used to access\n",
@@ -42,7 +50,11 @@
    "cell_type": "code",
    "execution_count": 3,
    "id": "ffd542f2",
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# One of the most useful examples for how to use R is reading in data directly\n",
@@ -59,7 +71,11 @@
    "cell_type": "code",
    "execution_count": 4,
    "id": "d8210bb7",
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [
     {
      "data": {
@@ -137,7 +153,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "541af031",
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": []
   }